diff options
Diffstat (limited to 'sci-biology')
146 files changed, 1324 insertions, 1093 deletions
diff --git a/sci-biology/ApE/metadata.xml b/sci-biology/ApE/metadata.xml index 7a38bb900964..83d00b14c8d4 100644 --- a/sci-biology/ApE/metadata.xml +++ b/sci-biology/ApE/metadata.xml @@ -1,5 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <!-- maintainer-needed --> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/GBrowse/metadata.xml b/sci-biology/GBrowse/metadata.xml index 1473cc001b3d..4ab248b5e412 100644 --- a/sci-biology/GBrowse/metadata.xml +++ b/sci-biology/GBrowse/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> -<maintainer type="project"> + <maintainer type="project"> <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> -</maintainer> -<upstream> + </maintainer> + <upstream> <remote-id type="cpan">GBrowse</remote-id> -</upstream> -</pkgmetadata> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/HTSeq/metadata.xml b/sci-biology/HTSeq/metadata.xml index 1b5a1245ecb9..498386657804 100644 --- a/sci-biology/HTSeq/metadata.xml +++ b/sci-biology/HTSeq/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="pypi">HTSeq</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="pypi">HTSeq</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/STAR/metadata.xml b/sci-biology/STAR/metadata.xml index def338693901..7daef842c2ea 100644 --- a/sci-biology/STAR/metadata.xml +++ b/sci-biology/STAR/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">alexdobin/STAR</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="github">alexdobin/STAR</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/aaindex/metadata.xml b/sci-biology/aaindex/metadata.xml index ffe91c9020d6..7be111eff816 100644 --- a/sci-biology/aaindex/metadata.xml +++ b/sci-biology/aaindex/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> Amino acid indices and similarity matrices maintained at Kyoto University. An amino acid index is a set of 20 numerical values representing any of the different physicochemical and biological @@ -22,4 +22,6 @@ acid mutation matrices together with the result of cluster analysis. This section currently contains 83 matrices. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml index 47116e507d89..d76b0cfee9bb 100644 --- a/sci-biology/abyss/metadata.xml +++ b/sci-biology/abyss/metadata.xml @@ -1,18 +1,19 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <maintainer type="project"> - <email>haskell@gentoo.org</email> - <name>Gentoo Haskell</name> - </maintainer> - <use> - <flag name="misc-haskell">build abyss-samtobreak tool, pull in haskell toolchain</flag> - </use> - <upstream> - <remote-id type="github">bcgsc/abyss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <maintainer type="project"> + <email>haskell@gentoo.org</email> + <name>Gentoo Haskell</name> + </maintainer> + <upstream> + <remote-id type="github">bcgsc/abyss</remote-id> + </upstream> + <use> + <flag name="misc-haskell">build abyss-samtobreak tool, pull in haskell toolchain</flag> + </use> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/amap/amap-2.2-r3.ebuild b/sci-biology/amap/amap-2.2-r3.ebuild index 075963104e3f..b1503814b48f 100644 --- a/sci-biology/amap/amap-2.2-r3.ebuild +++ b/sci-biology/amap/amap-2.2-r3.ebuild @@ -8,7 +8,7 @@ inherit java-pkg-opt-2 java-ant-2 toolchain-funcs MY_P=${PN}.${PV} DESCRIPTION="Protein multiple-alignment-based sequence annealing" -HOMEPAGE="https://web.archive.org/web/20060902044446/http://bio.math.berkeley.edu/amap/" +HOMEPAGE="https://bio.math.berkeley.edu/amap/" SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz" LICENSE="GPL-2" diff --git a/sci-biology/amap/metadata.xml b/sci-biology/amap/metadata.xml index e051c9b41035..df75f9d83fc3 100644 --- a/sci-biology/amap/metadata.xml +++ b/sci-biology/amap/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> -<maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> -</maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/augustus/augustus-2.5.5.ebuild b/sci-biology/augustus/augustus-2.5.5.ebuild index 9ce5c784ca15..4aee07885522 100644 --- a/sci-biology/augustus/augustus-2.5.5.ebuild +++ b/sci-biology/augustus/augustus-2.5.5.ebuild @@ -6,7 +6,7 @@ EAPI=7 inherit toolchain-funcs DESCRIPTION="Eukaryotic gene predictor" -HOMEPAGE="http://bioinf.uni-greifswald.de/augustus/" +HOMEPAGE="https://augustus.gobics.de/" SRC_URI="http://augustus.gobics.de/binaries/${PN}.${PV}.tar.gz" LICENSE="Artistic" diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/augustus/metadata.xml +++ b/sci-biology/augustus/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/bamtools/metadata.xml b/sci-biology/bamtools/metadata.xml index 9aa0cee0cf72..0dbd3eef757b 100644 --- a/sci-biology/bamtools/metadata.xml +++ b/sci-biology/bamtools/metadata.xml @@ -1,12 +1,13 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription>BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.</longdescription> - <upstream> - <remote-id type="github">pezmaster31/bamtools</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription>BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.</longdescription> + <upstream> + <remote-id type="github">pezmaster31/bamtools</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/bcftools/metadata.xml b/sci-biology/bcftools/metadata.xml index 0421097960c1..2d97cce6ecef 100644 --- a/sci-biology/bcftools/metadata.xml +++ b/sci-biology/bcftools/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">samtools/bcftools</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="github">samtools/bcftools</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest index 5dc912159a45..d2d1a7150f72 100644 --- a/sci-biology/bedtools/Manifest +++ b/sci-biology/bedtools/Manifest @@ -1 +1,2 @@ DIST bedtools-2.29.2.tar.gz 20646485 BLAKE2B cdfff7a0f5300f31c2487e98bd28dc7e8b7f3575a098947c2c7b3a6e30272a80d35f07997d3a00bd42d91bf60899f32358b25b054b6f40b761cc66e2788508b3 SHA512 138ff029995e9889d2e43f884fa15bb5614d11cf75dfe18e2999aad0915e80f49444e67c9934c92ca8e28caad399394b493db8a1bee9f5304413a8c41c22c6d5 +DIST bedtools-2.30.0.tar.gz 20648577 BLAKE2B 042bc31e846455cb1c20199f7a27a3850851f7c256a45b1e674c7aa48ecedc211b0fdfc5e25f915b588f21447e757ebff2bba16a65905bb10d3c88e4b17b1db1 SHA512 3993243cc3db12d194d6220aeae200e6af843d6d32d4e5a9a82d04c9d119f8ed47e618e87241edfa82cfac081bc9a40ada18f097d21b0cafc5f912ae012701c9 diff --git a/sci-biology/bedtools/bedtools-2.30.0.ebuild b/sci-biology/bedtools/bedtools-2.30.0.ebuild new file mode 100644 index 000000000000..f1f74b6bb947 --- /dev/null +++ b/sci-biology/bedtools/bedtools-2.30.0.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{6,7,8,9,10} ) + +inherit python-any-r1 toolchain-funcs + +DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats" +HOMEPAGE="https://bedtools.readthedocs.io/" +SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND=" + app-arch/bzip2 + app-arch/xz-utils + sys-libs/zlib" +DEPEND="${RDEPEND}" +BDEPEND=" + ${PYTHON_DEPS} + test? ( >=sci-biology/samtools-1.10:0 )" + +S="${WORKDIR}"/${PN}2 + +# bedtools2 has a *terrible* build system and development practices. +# Upstream has forked htslib 1.9 and extended it by adding clever callbacks +# that make unbundling it nigh impossible. There are no signs of upstream porting +# their fork to 1.10, which means we're stuck with the bundled version. +PATCHES=( + "${FILESDIR}"/${PN}-2.29.2-buildsystem.patch + "${FILESDIR}"/${PN}-2.29.2-python.patch +) + +src_configure() { + tc-export AR CC CXX RANLIB +} + +src_install() { + default + + insinto /usr/share/${PN} + doins -r genomes +} diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml index ec82800df5dd..81bf9e1b3f8f 100644 --- a/sci-biology/bedtools/metadata.xml +++ b/sci-biology/bedtools/metadata.xml @@ -1,12 +1,13 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="google-code">bedtools</remote-id> - <remote-id type="github">arq5x/bedtools2</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="google-code">bedtools</remote-id> + <remote-id type="github">arq5x/bedtools2</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/bfast/metadata.xml b/sci-biology/bfast/metadata.xml index 933dea84e1b3..c012beb6bbef 100644 --- a/sci-biology/bfast/metadata.xml +++ b/sci-biology/bfast/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">bfast</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">bfast</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/biogrep/metadata.xml b/sci-biology/biogrep/metadata.xml index 8417d1580d40..df75f9d83fc3 100644 --- a/sci-biology/biogrep/metadata.xml +++ b/sci-biology/biogrep/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/biopandas/metadata.xml b/sci-biology/biopandas/metadata.xml index f23da0b1ebe2..af330140bacc 100644 --- a/sci-biology/biopandas/metadata.xml +++ b/sci-biology/biopandas/metadata.xml @@ -1,16 +1,13 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="pypi">BioPandas</remote-id> - <maintainer status="unknown"> - <email>mail@sebastianraschka.com</email> - <name>Sebastian Raschka</name> - </maintainer> - <remote-id type="github">rasbt/biopandas</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="pypi">BioPandas</remote-id> + <remote-id type="github">rasbt/biopandas</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild index facab7d5ffbe..7e330b5a99c5 100644 --- a/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild +++ b/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild @@ -11,7 +11,7 @@ DIST_VERSION=1.006900 inherit perl-module DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema" -HOMEPAGE="http://www.bioperl.org/" +HOMEPAGE="https://www.bioperl.org/" SLOT="0" KEYWORDS="~amd64 ~x86" diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild index e6f0c45958a9..46dec6540fc0 100644 --- a/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild +++ b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild @@ -11,7 +11,7 @@ MODULE_VERSION=1.006900 inherit perl-module DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema" -HOMEPAGE="http://www.bioperl.org/" +HOMEPAGE="https://www.bioperl.org/" SLOT="0" KEYWORDS="amd64 x86" diff --git a/sci-biology/bioperl-db/metadata.xml b/sci-biology/bioperl-db/metadata.xml index 09e1cb381b7f..8a653f56f88a 100644 --- a/sci-biology/bioperl-db/metadata.xml +++ b/sci-biology/bioperl-db/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="cpan">BioPerl-DB</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="cpan">BioPerl-DB</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild b/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild index 65a72e06634f..82bd3ce5e4fa 100644 --- a/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild +++ b/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild @@ -11,7 +11,7 @@ MODULE_VERSION=1.006900 inherit perl-module DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks" -HOMEPAGE="http://www.bioperl.org/" +HOMEPAGE="https://www.bioperl.org/" SLOT="0" KEYWORDS="amd64 x86" diff --git a/sci-biology/bioperl-network/metadata.xml b/sci-biology/bioperl-network/metadata.xml index 754b8d123313..0ce330797972 100644 --- a/sci-biology/bioperl-network/metadata.xml +++ b/sci-biology/bioperl-network/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="cpan">BioPerl-Network</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="cpan">BioPerl-Network</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild index e5dc816bc78a..4142ed031f73 100644 --- a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild +++ b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild @@ -11,7 +11,7 @@ MODULE_VERSION=1.006900 inherit perl-module DESCRIPTION="Perl wrapper modules for key bioinformatics applications" -HOMEPAGE="http://www.bioperl.org/" +HOMEPAGE="https://www.bioperl.org/" SLOT="0" KEYWORDS="amd64 x86" diff --git a/sci-biology/bioperl-run/metadata.xml b/sci-biology/bioperl-run/metadata.xml index 5fccf50862ad..66faab6f94aa 100644 --- a/sci-biology/bioperl-run/metadata.xml +++ b/sci-biology/bioperl-run/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="cpan">BioPerl-Run</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="cpan">BioPerl-Run</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/bioperl/bioperl-1.6.9.ebuild b/sci-biology/bioperl/bioperl-1.6.9.ebuild index d2519a0d30b6..d63c03b8df18 100644 --- a/sci-biology/bioperl/bioperl-1.6.9.ebuild +++ b/sci-biology/bioperl/bioperl-1.6.9.ebuild @@ -12,7 +12,7 @@ SUBPROJECTS="+db +network +run" MIN_PV=$PV DESCRIPTION="Perl tools for bioinformatics - Core modules" -HOMEPAGE="http://www.bioperl.org/" +HOMEPAGE="https://www.bioperl.org/" SLOT="0" KEYWORDS="amd64 x86" IUSE="-minimal graphviz sqlite ${SUBPROJECTS}" diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml index 1cd5db0e9619..8f98d9aa97af 100644 --- a/sci-biology/bioperl/metadata.xml +++ b/sci-biology/bioperl/metadata.xml @@ -1,16 +1,17 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="run">Install sci-biology/bioperl-run</flag> - <flag name="network">Install sci-biology/bioperl-run</flag> - <flag name="db">Install sci-biology/bioperl-run</flag> - </use> - <upstream> - <remote-id type="cpan">BioPerl</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="cpan">BioPerl</remote-id> + </upstream> + <use> + <flag name="run">Install sci-biology/bioperl-run</flag> + <flag name="network">Install sci-biology/bioperl-run</flag> + <flag name="db">Install sci-biology/bioperl-run</flag> + </use> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml index 7ffa3b15e08e..22810094bfbc 100644 --- a/sci-biology/biopython/metadata.xml +++ b/sci-biology/biopython/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="pypi">biopython</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="pypi">biopython</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/biosql/biosql-1.0.1-r1.ebuild b/sci-biology/biosql/biosql-1.0.1-r1.ebuild index 6508d6a3a2e8..a68a18681783 100644 --- a/sci-biology/biosql/biosql-1.0.1-r1.ebuild +++ b/sci-biology/biosql/biosql-1.0.1-r1.ebuild @@ -4,7 +4,7 @@ EAPI=6 DESCRIPTION="A generic bioinformatics relational database model" -HOMEPAGE="http://www.biosql.org/" +HOMEPAGE="https://www.biosql.org/" SRC_URI="http://biosql.org/DIST/${P}.tar.bz2" LICENSE="LGPL-3" diff --git a/sci-biology/biosql/metadata.xml b/sci-biology/biosql/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/biosql/metadata.xml +++ b/sci-biology/biosql/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/blat/metadata.xml b/sci-biology/blat/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/blat/metadata.xml +++ b/sci-biology/blat/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml index 71e8d3bb8e0f..78e859bc0af2 100644 --- a/sci-biology/bowtie/metadata.xml +++ b/sci-biology/bowtie/metadata.xml @@ -1,16 +1,17 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">bowtie-bio</remote-id> - </upstream> - <use> - <flag name="tbb">Enables building bowtie with the Intel + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">bowtie-bio</remote-id> + </upstream> + <use> + <flag name="tbb">Enables building bowtie with the Intel Threading Building Blocks from <pkg>dev-cpp/tbb</pkg>. This flag is recommended.</flag> - </use> -</pkgmetadata> + </use> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml index ceb43ead2a3f..cbf83bbe5db4 100644 --- a/sci-biology/bwa/metadata.xml +++ b/sci-biology/bwa/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">bio-bwa</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">bio-bwa</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml index 1f3b075216dd..82f08d1e9711 100644 --- a/sci-biology/cd-hit/metadata.xml +++ b/sci-biology/cd-hit/metadata.xml @@ -1,11 +1,11 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> CD-HIT is a very widely used program for clustering and comparing large sets of protein or nucleotide sequences. CD-HIT is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the @@ -20,8 +20,9 @@ a threshold. CD-HIT-454 is a program to identify natural and artificial duplicates from pyrosequencing reads. The usage of other programs and scripts can be found in CD-HIT user's guide. </longdescription> - <upstream> - <remote-id type="google-code">cdhit</remote-id> - <remote-id type="github">weizhongli/cdhit</remote-id> - </upstream> -</pkgmetadata> + <upstream> + <remote-id type="google-code">cdhit</remote-id> + <remote-id type="github">weizhongli/cdhit</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/clustal-omega/metadata.xml b/sci-biology/clustal-omega/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/clustal-omega/metadata.xml +++ b/sci-biology/clustal-omega/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml index ffe2c4efec87..0fb85bdab340 100644 --- a/sci-biology/clustalw-mpi/metadata.xml +++ b/sci-biology/clustalw-mpi/metadata.xml @@ -1,12 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="mpi-njtree">Use MPI (as opposed to serial) code for computing neighbor-joining trees</flag> - <flag name="static-pairalign">Use static (as opposed to dynamic) scheduling for pair alignments</flag> - </use> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <use> + <flag name="mpi-njtree">Use MPI (as opposed to serial) code for computing neighbor-joining trees</flag> + <flag name="static-pairalign">Use static (as opposed to dynamic) scheduling for pair alignments</flag> + </use> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/clustalw/metadata.xml b/sci-biology/clustalw/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/clustalw/metadata.xml +++ b/sci-biology/clustalw/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/clustalx/metadata.xml b/sci-biology/clustalx/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/clustalx/metadata.xml +++ b/sci-biology/clustalx/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/consed/metadata.xml +++ b/sci-biology/consed/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/cutg/metadata.xml b/sci-biology/cutg/metadata.xml index 0f8a9b77b269..780a70dbd9e1 100644 --- a/sci-biology/cutg/metadata.xml +++ b/sci-biology/cutg/metadata.xml @@ -1,15 +1,17 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> Codon usage tables maintained at the Kazusa DNA Research Institute. Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/dialign-tx/metadata.xml b/sci-biology/dialign-tx/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/dialign-tx/metadata.xml +++ b/sci-biology/dialign-tx/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/dialign2/metadata.xml b/sci-biology/dialign2/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/dialign2/metadata.xml +++ b/sci-biology/dialign2/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/diya/metadata.xml b/sci-biology/diya/metadata.xml index 37bde911b940..521f2f0ef284 100644 --- a/sci-biology/diya/metadata.xml +++ b/sci-biology/diya/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">diyg</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">diyg</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/elph/metadata.xml b/sci-biology/elph/metadata.xml index 979dde87e15d..e7cb5e9a7697 100644 --- a/sci-biology/elph/metadata.xml +++ b/sci-biology/elph/metadata.xml @@ -1,15 +1,17 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> ELPH is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences. The program takes as input a set containing anywhere from a few dozen to thousands of sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/embassy-cbstools/metadata.xml b/sci-biology/embassy-cbstools/metadata.xml index d1b9a7602ec2..1c005db8c395 100644 --- a/sci-biology/embassy-cbstools/metadata.xml +++ b/sci-biology/embassy-cbstools/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/embassy-clustalomega/metadata.xml b/sci-biology/embassy-clustalomega/metadata.xml index d1b9a7602ec2..1c005db8c395 100644 --- a/sci-biology/embassy-clustalomega/metadata.xml +++ b/sci-biology/embassy-clustalomega/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/embassy-domainatrix/metadata.xml b/sci-biology/embassy-domainatrix/metadata.xml index d1b9a7602ec2..1c005db8c395 100644 --- a/sci-biology/embassy-domainatrix/metadata.xml +++ b/sci-biology/embassy-domainatrix/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/embassy-domalign/metadata.xml b/sci-biology/embassy-domalign/metadata.xml index d1b9a7602ec2..1c005db8c395 100644 --- a/sci-biology/embassy-domalign/metadata.xml +++ b/sci-biology/embassy-domalign/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/embassy-domsearch/metadata.xml b/sci-biology/embassy-domsearch/metadata.xml index d1b9a7602ec2..1c005db8c395 100644 --- a/sci-biology/embassy-domsearch/metadata.xml +++ b/sci-biology/embassy-domsearch/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/embassy-emnu/metadata.xml b/sci-biology/embassy-emnu/metadata.xml index d1b9a7602ec2..1c005db8c395 100644 --- a/sci-biology/embassy-emnu/metadata.xml +++ b/sci-biology/embassy-emnu/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/embassy-esim4/metadata.xml b/sci-biology/embassy-esim4/metadata.xml index d1b9a7602ec2..1c005db8c395 100644 --- a/sci-biology/embassy-esim4/metadata.xml +++ b/sci-biology/embassy-esim4/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/embassy-hmmer/metadata.xml b/sci-biology/embassy-hmmer/metadata.xml index d1b9a7602ec2..1c005db8c395 100644 --- a/sci-biology/embassy-hmmer/metadata.xml +++ b/sci-biology/embassy-hmmer/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/embassy-iprscan/metadata.xml b/sci-biology/embassy-iprscan/metadata.xml index d1b9a7602ec2..1c005db8c395 100644 --- a/sci-biology/embassy-iprscan/metadata.xml +++ b/sci-biology/embassy-iprscan/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/embassy-mse/metadata.xml b/sci-biology/embassy-mse/metadata.xml index d1b9a7602ec2..1c005db8c395 100644 --- a/sci-biology/embassy-mse/metadata.xml +++ b/sci-biology/embassy-mse/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/embassy-phylipnew/metadata.xml b/sci-biology/embassy-phylipnew/metadata.xml index d1b9a7602ec2..1c005db8c395 100644 --- a/sci-biology/embassy-phylipnew/metadata.xml +++ b/sci-biology/embassy-phylipnew/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/embassy-signature/metadata.xml b/sci-biology/embassy-signature/metadata.xml index d1b9a7602ec2..1c005db8c395 100644 --- a/sci-biology/embassy-signature/metadata.xml +++ b/sci-biology/embassy-signature/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/embassy-structure/metadata.xml b/sci-biology/embassy-structure/metadata.xml index d1b9a7602ec2..1c005db8c395 100644 --- a/sci-biology/embassy-structure/metadata.xml +++ b/sci-biology/embassy-structure/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/embassy-topo/metadata.xml b/sci-biology/embassy-topo/metadata.xml index d1b9a7602ec2..1c005db8c395 100644 --- a/sci-biology/embassy-topo/metadata.xml +++ b/sci-biology/embassy-topo/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/embassy-vienna/metadata.xml b/sci-biology/embassy-vienna/metadata.xml index d1b9a7602ec2..1c005db8c395 100644 --- a/sci-biology/embassy-vienna/metadata.xml +++ b/sci-biology/embassy-vienna/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/embassy/metadata.xml b/sci-biology/embassy/metadata.xml index d1b9a7602ec2..1c005db8c395 100644 --- a/sci-biology/embassy/metadata.xml +++ b/sci-biology/embassy/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/emboss/metadata.xml b/sci-biology/emboss/metadata.xml index 7443e66b770f..cb2a85929c5a 100644 --- a/sci-biology/emboss/metadata.xml +++ b/sci-biology/emboss/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user @@ -18,7 +18,8 @@ analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages. </longdescription> - <upstream> - <remote-id type="sourceforge">emboss</remote-id> - </upstream> -</pkgmetadata> + <upstream> + <remote-id type="sourceforge">emboss</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/eugene/metadata.xml b/sci-biology/eugene/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/eugene/metadata.xml +++ b/sci-biology/eugene/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/exonerate/metadata.xml b/sci-biology/exonerate/metadata.xml index b64950792715..66ea6756a198 100644 --- a/sci-biology/exonerate/metadata.xml +++ b/sci-biology/exonerate/metadata.xml @@ -1,11 +1,13 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="utils">Install all utilities</flag> - </use> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <use> + <flag name="utils">Install all utilities</flag> + </use> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/express/metadata.xml b/sci-biology/express/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/express/metadata.xml +++ b/sci-biology/express/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/fasta/metadata.xml b/sci-biology/fasta/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/fasta/metadata.xml +++ b/sci-biology/fasta/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/fasttree/metadata.xml b/sci-biology/fasttree/metadata.xml index 674816fe4822..2348d7f3d819 100644 --- a/sci-biology/fasttree/metadata.xml +++ b/sci-biology/fasttree/metadata.xml @@ -1,14 +1,16 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="double-precision"> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <use> + <flag name="double-precision"> use double precision instead of single-precision floating point (2x memroy required) </flag> - </use> -</pkgmetadata> + </use> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/fastx_toolkit/metadata.xml b/sci-biology/fastx_toolkit/metadata.xml index 880cea0165ff..4c9df495eccf 100644 --- a/sci-biology/fastx_toolkit/metadata.xml +++ b/sci-biology/fastx_toolkit/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <upstream> - <remote-id type="github">agordon/fastx_toolkit</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">agordon/fastx_toolkit</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/finchtv/finchtv-1.3.1-r2.ebuild b/sci-biology/finchtv/finchtv-1.3.1-r2.ebuild deleted file mode 100644 index 8794cd1258be..000000000000 --- a/sci-biology/finchtv/finchtv-1.3.1-r2.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -MY_PV="${PV//./_}" -MY_P=${PN}_${MY_PV} - -DESCRIPTION="Graphical viewer for chromatogram files" -HOMEPAGE="https://www.geospiza.com/finchtv/" -SRC_URI="http://www.geospiza.com/finchtv/download/programs/linux/${MY_P}.tar.gz" - -LICENSE="finchtv" -SLOT="0" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="" - -S="${WORKDIR}/${MY_P}" - -QA_PREBUILT="opt/bin/*" - -src_install() { - exeinto /opt/bin - doexe finchtv - dodoc ReleaseNotes.txt - dohtml -r Help/* - insinto /usr/share/doc/${PN} - doins -r SampleData -} diff --git a/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild b/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild index f96f18677e9f..372209987d9b 100644 --- a/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild +++ b/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 -inherit eutils +inherit desktop MY_PV="${PV//./_}" MY_P=${PN}_${MY_PV} @@ -14,8 +14,7 @@ SRC_URI="http://www.geospiza.com/finchtv/download/programs/linux/${MY_P}.tar.gz" LICENSE="finchtv" SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" S="${WORKDIR}/${MY_P}" @@ -26,11 +25,13 @@ src_install() { doexe finchtv dodoc ReleaseNotes.txt - docinto html - dodoc -r Help/* - insinto /usr/share/doc/${PN} - doins -r SampleData + docinto examples + dodoc -r SampleData/. + docompress -x /usr/share/doc/${PF}/examples + + docinto html + dodoc -r Help/. newicon Help/media/FinchTV_Mac_App.png ${PN}.png } diff --git a/sci-biology/finchtv/metadata.xml b/sci-biology/finchtv/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/finchtv/metadata.xml +++ b/sci-biology/finchtv/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/foldingathome/metadata.xml b/sci-biology/foldingathome/metadata.xml index e051c9b41035..df75f9d83fc3 100644 --- a/sci-biology/foldingathome/metadata.xml +++ b/sci-biology/foldingathome/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> -<maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> -</maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/gatk/metadata.xml b/sci-biology/gatk/metadata.xml index 8c1bb65774cc..9e85fb274ecb 100644 --- a/sci-biology/gatk/metadata.xml +++ b/sci-biology/gatk/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">broadgsa/gatk</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="github">broadgsa/gatk</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/gibbs/metadata.xml b/sci-biology/gibbs/metadata.xml index fc9e1d2b4594..7918c369f4cb 100644 --- a/sci-biology/gibbs/metadata.xml +++ b/sci-biology/gibbs/metadata.xml @@ -1,13 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> The Gibbs motif sampler stochastically examines candidate alignments in an effort to find the best alignment as measured by the maximum a posteriori (MAP) log-likelihood ratio. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/glimmer/metadata.xml b/sci-biology/glimmer/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/glimmer/metadata.xml +++ b/sci-biology/glimmer/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/glimmerhmm/metadata.xml b/sci-biology/glimmerhmm/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/glimmerhmm/metadata.xml +++ b/sci-biology/glimmerhmm/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/gmap/metadata.xml b/sci-biology/gmap/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/gmap/metadata.xml +++ b/sci-biology/gmap/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml index 8417d1580d40..df75f9d83fc3 100644 --- a/sci-biology/hmmer/metadata.xml +++ b/sci-biology/hmmer/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/iedera/metadata.xml b/sci-biology/iedera/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/iedera/metadata.xml +++ b/sci-biology/iedera/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/infernal/metadata.xml b/sci-biology/infernal/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/infernal/metadata.xml +++ b/sci-biology/infernal/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/iqpnni/metadata.xml b/sci-biology/iqpnni/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/iqpnni/metadata.xml +++ b/sci-biology/iqpnni/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/kalign/metadata.xml b/sci-biology/kalign/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/kalign/metadata.xml +++ b/sci-biology/kalign/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/kallisto/metadata.xml b/sci-biology/kallisto/metadata.xml index 03ad8ef865a9..e1341b388139 100644 --- a/sci-biology/kallisto/metadata.xml +++ b/sci-biology/kallisto/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">pachterlab/kallisto</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="github">pachterlab/kallisto</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/lagan/metadata.xml b/sci-biology/lagan/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/lagan/metadata.xml +++ b/sci-biology/lagan/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/libgtextutils/metadata.xml b/sci-biology/libgtextutils/metadata.xml index 38108be67e14..af21e416ac2e 100644 --- a/sci-biology/libgtextutils/metadata.xml +++ b/sci-biology/libgtextutils/metadata.xml @@ -1,12 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@gmail.com</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="person"> + <email>mmokrejs@gmail.com</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/mafft/metadata.xml b/sci-biology/mafft/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/mafft/metadata.xml +++ b/sci-biology/mafft/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/maq/metadata.xml b/sci-biology/maq/metadata.xml index 0b39d2a8530d..c27112c30bf1 100644 --- a/sci-biology/maq/metadata.xml +++ b/sci-biology/maq/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">maq</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">maq</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/maqview/metadata.xml b/sci-biology/maqview/metadata.xml index 0b39d2a8530d..c27112c30bf1 100644 --- a/sci-biology/maqview/metadata.xml +++ b/sci-biology/maqview/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">maq</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">maq</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/mcl/metadata.xml b/sci-biology/mcl/metadata.xml index 25048faf1643..873d47acfe8e 100644 --- a/sci-biology/mcl/metadata.xml +++ b/sci-biology/mcl/metadata.xml @@ -1,11 +1,13 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="blast">Add support for NCBI BLAST data</flag> - </use> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <use> + <flag name="blast">Add support for NCBI BLAST data</flag> + </use> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml index 0704cef4806d..17babc81cfc2 100644 --- a/sci-biology/mira/metadata.xml +++ b/sci-biology/mira/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">mira-assembler</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">mira-assembler</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/mosaik/metadata.xml b/sci-biology/mosaik/metadata.xml index a3eca9b62b1c..59f1f5fae1f2 100644 --- a/sci-biology/mosaik/metadata.xml +++ b/sci-biology/mosaik/metadata.xml @@ -1,12 +1,13 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="google-code">mosaik-aligner</remote-id> - <remote-id type="github">wanpinglee/MOSAIK</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="google-code">mosaik-aligner</remote-id> + <remote-id type="github">wanpinglee/MOSAIK</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/mothur/metadata.xml b/sci-biology/mothur/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/mothur/metadata.xml +++ b/sci-biology/mothur/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml index ca6afd95a12e..eff0dfec57e9 100644 --- a/sci-biology/mrbayes/metadata.xml +++ b/sci-biology/mrbayes/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a @@ -15,7 +15,8 @@ impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. </longdescription> - <upstream> - <remote-id type="sourceforge">mrbayes</remote-id> - </upstream> -</pkgmetadata> + <upstream> + <remote-id type="sourceforge">mrbayes</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/mummer/metadata.xml b/sci-biology/mummer/metadata.xml index 4a3fe8e7bd15..3ac5022a3987 100644 --- a/sci-biology/mummer/metadata.xml +++ b/sci-biology/mummer/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">mummer</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">mummer</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/muscle/metadata.xml b/sci-biology/muscle/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/muscle/metadata.xml +++ b/sci-biology/muscle/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/ncbi-tools/metadata.xml b/sci-biology/ncbi-tools/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/ncbi-tools/metadata.xml +++ b/sci-biology/ncbi-tools/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/newick-utils/metadata.xml b/sci-biology/newick-utils/metadata.xml index d9bc91509874..a9d368a56f17 100644 --- a/sci-biology/newick-utils/metadata.xml +++ b/sci-biology/newick-utils/metadata.xml @@ -1,11 +1,13 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="xml">Uses <pkg>dev-libs/libxml2</pkg> to handle ornaments</flag> - </use> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <use> + <flag name="xml">Uses <pkg>dev-libs/libxml2</pkg> to handle ornaments</flag> + </use> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/njplot/metadata.xml b/sci-biology/njplot/metadata.xml index 2a3eb3140966..74bff1f3c007 100644 --- a/sci-biology/njplot/metadata.xml +++ b/sci-biology/njplot/metadata.xml @@ -1,15 +1,17 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> NJplot is a tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/pals/metadata.xml b/sci-biology/pals/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/pals/metadata.xml +++ b/sci-biology/pals/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/paml/metadata.xml b/sci-biology/paml/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/paml/metadata.xml +++ b/sci-biology/paml/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/phrap/metadata.xml b/sci-biology/phrap/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/phrap/metadata.xml +++ b/sci-biology/phrap/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/phred/metadata.xml b/sci-biology/phred/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/phred/metadata.xml +++ b/sci-biology/phred/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/phylip/metadata.xml b/sci-biology/phylip/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/phylip/metadata.xml +++ b/sci-biology/phylip/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/phyml/metadata.xml b/sci-biology/phyml/metadata.xml index d4e4a77f868c..66886740bfe9 100644 --- a/sci-biology/phyml/metadata.xml +++ b/sci-biology/phyml/metadata.xml @@ -1,14 +1,16 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription lang="en"> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription lang="en"> Phyml is a simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Given input sequence files, it estimates phylogenies using maximum likelihood, and is capable of processing large amounts of phylogenetic data. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml index 34f79a25054b..4905c9f583d0 100644 --- a/sci-biology/picard/metadata.xml +++ b/sci-biology/picard/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">picard</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">picard</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/piler/metadata.xml b/sci-biology/piler/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/piler/metadata.xml +++ b/sci-biology/piler/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/pilercr/metadata.xml b/sci-biology/pilercr/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/pilercr/metadata.xml +++ b/sci-biology/pilercr/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/plink/metadata.xml b/sci-biology/plink/metadata.xml index 8417d1580d40..df75f9d83fc3 100644 --- a/sci-biology/plink/metadata.xml +++ b/sci-biology/plink/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/poa/metadata.xml b/sci-biology/poa/metadata.xml index 229e2f246a80..bbacaa44c2ef 100644 --- a/sci-biology/poa/metadata.xml +++ b/sci-biology/poa/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">poamsa</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">poamsa</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/prank/metadata.xml b/sci-biology/prank/metadata.xml index 8d1d75556076..1daf9bb68a41 100644 --- a/sci-biology/prank/metadata.xml +++ b/sci-biology/prank/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="google-code">prank-msa</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="google-code">prank-msa</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/primer3/metadata.xml b/sci-biology/primer3/metadata.xml index b80de21c3321..7b8c1c4952ee 100644 --- a/sci-biology/primer3/metadata.xml +++ b/sci-biology/primer3/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> Primer3 picks primers for PCR reactions, considering: oligonucleotide melting temperature, size, GC content, and primer-dimer possibilities; PCR product size; positional constraints within the source sequence; @@ -13,7 +13,8 @@ user-specifiable as constraints, and some are specifiable as terms in an objective function that characterizes an optimal primer pair. </longdescription> - <upstream> - <remote-id type="sourceforge">primer3</remote-id> - </upstream> -</pkgmetadata> + <upstream> + <remote-id type="sourceforge">primer3</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/prints/metadata.xml b/sci-biology/prints/metadata.xml index af3ff0786e0c..e911b4187fde 100644 --- a/sci-biology/prints/metadata.xml +++ b/sci-biology/prints/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> A protein motif fingerprint database maintained at the University of Manchester. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by @@ -16,4 +16,6 @@ full diagnostic potency deriving from the mutual context provided by motif neighbours. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/probcons/metadata.xml b/sci-biology/probcons/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/probcons/metadata.xml +++ b/sci-biology/probcons/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/prodigal/metadata.xml b/sci-biology/prodigal/metadata.xml index e086d08df6f7..006eb05162f6 100644 --- a/sci-biology/prodigal/metadata.xml +++ b/sci-biology/prodigal/metadata.xml @@ -1,12 +1,13 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="google-code">prodigal</remote-id> - <remote-id type="github">hyattpd/Prodigal</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="google-code">prodigal</remote-id> + <remote-id type="github">hyattpd/Prodigal</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/profphd/metadata.xml b/sci-biology/profphd/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/profphd/metadata.xml +++ b/sci-biology/profphd/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/prosite/metadata.xml b/sci-biology/prosite/metadata.xml index 59076478066f..dec7318bceb4 100644 --- a/sci-biology/prosite/metadata.xml +++ b/sci-biology/prosite/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> A protein families and domains database maintained at the Swiss Institude for Bioinformatics. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which @@ -15,4 +15,6 @@ documentation providing background information on the structure and function of these proteins. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/psipred/metadata.xml b/sci-biology/psipred/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/psipred/metadata.xml +++ b/sci-biology/psipred/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml index d9da2562da6c..6201566dac14 100644 --- a/sci-biology/pysam/metadata.xml +++ b/sci-biology/pysam/metadata.xml @@ -1,13 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="google-code">pysam</remote-id> - <remote-id type="github">pysam-developers/pysam</remote-id> - <remote-id type="pypi">pysam</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="google-code">pysam</remote-id> + <remote-id type="github">pysam-developers/pysam</remote-id> + <remote-id type="pypi">pysam</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/qrna/metadata.xml b/sci-biology/qrna/metadata.xml index 8417d1580d40..df75f9d83fc3 100644 --- a/sci-biology/qrna/metadata.xml +++ b/sci-biology/qrna/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/raxml/metadata.xml b/sci-biology/raxml/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/raxml/metadata.xml +++ b/sci-biology/raxml/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/rebase/metadata.xml b/sci-biology/rebase/metadata.xml index dbd090188c93..9746afc4e112 100644 --- a/sci-biology/rebase/metadata.xml +++ b/sci-biology/rebase/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> The Restriction Enzyme data BASE is a collection of information about restriction enzymes and related proteins. It is maintained by New England Biolabs. It contains published and unpublished references, @@ -16,4 +16,6 @@ putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/recon/metadata.xml b/sci-biology/recon/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/recon/metadata.xml +++ b/sci-biology/recon/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/repeatmasker-libraries/metadata.xml b/sci-biology/repeatmasker-libraries/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/repeatmasker-libraries/metadata.xml +++ b/sci-biology/repeatmasker-libraries/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/repeatmasker/metadata.xml +++ b/sci-biology/repeatmasker/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/rmblast/metadata.xml b/sci-biology/rmblast/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/rmblast/metadata.xml +++ b/sci-biology/rmblast/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/rnaview/metadata.xml b/sci-biology/rnaview/metadata.xml index cfffc1223753..978b71a0147c 100644 --- a/sci-biology/rnaview/metadata.xml +++ b/sci-biology/rnaview/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> The RNAView program generates 2-dimensional displays of RNA/DNA secondary structures with tertiary interactions. RNAView automatically identifies and classifies the types of base pairs that @@ -13,4 +13,6 @@ Westhof's (RNA (2001) 7, 499-512), convention for edge-to-edge hydrogen bonding interactions. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/samtools/metadata.xml b/sci-biology/samtools/metadata.xml index fe27db1184af..8d78af8e29e7 100644 --- a/sci-biology/samtools/metadata.xml +++ b/sci-biology/samtools/metadata.xml @@ -1,12 +1,13 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">samtools</remote-id> - <remote-id type="github">samtools/samtools</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">samtools</remote-id> + <remote-id type="github">samtools/samtools</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/seaview/metadata.xml b/sci-biology/seaview/metadata.xml index 14e26ee93445..d72e6d83b518 100644 --- a/sci-biology/seaview/metadata.xml +++ b/sci-biology/seaview/metadata.xml @@ -1,15 +1,17 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> SeaView is a graphical multiple sequence alignment editor developped by Manolo Gouy. SeaView is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW programs to locally improve the alignment. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/seqan/metadata.xml b/sci-biology/seqan/metadata.xml index 077f6458a927..4719f4b8ac09 100644 --- a/sci-biology/seqan/metadata.xml +++ b/sci-biology/seqan/metadata.xml @@ -1,11 +1,13 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="tools">Build and install SeqAn commandline tools, such as the Yara aligner</flag> - </use> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <use> + <flag name="tools">Build and install SeqAn commandline tools, such as the Yara aligner</flag> + </use> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/sibsim4/metadata.xml b/sci-biology/sibsim4/metadata.xml index 9445a4950bc0..0fc4f5eec70f 100644 --- a/sci-biology/sibsim4/metadata.xml +++ b/sci-biology/sibsim4/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">sibsim4</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">sibsim4</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/sim4/metadata.xml b/sci-biology/sim4/metadata.xml index 6366d6fb797e..09f16a4476fd 100644 --- a/sci-biology/sim4/metadata.xml +++ b/sci-biology/sim4/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects end matches when the two input sequences overlap at one end (i.e., the @@ -21,4 +21,6 @@ process is repeated with less stringent parameters on the unmatched fragments. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/stride/metadata.xml b/sci-biology/stride/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/stride/metadata.xml +++ b/sci-biology/stride/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/t-coffee/metadata.xml b/sci-biology/t-coffee/metadata.xml index b3853e6454a3..3f4e627e18f8 100644 --- a/sci-biology/t-coffee/metadata.xml +++ b/sci-biology/t-coffee/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures. @@ -14,4 +14,6 @@ estimate the level of consistency of each position within the new alignment with the rest of the alignments. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/transfac/metadata.xml b/sci-biology/transfac/metadata.xml index a8cecf4529c2..2627287ecbc1 100644 --- a/sci-biology/transfac/metadata.xml +++ b/sci-biology/transfac/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> TRANSFAC® is a database of eukaryotic transcription factors, of their genomic binding sites and DNA-binding profiles. TRANSFAC 3.2 is an old public version available at the European Bioinformatics Institute. @@ -13,4 +13,6 @@ offer public access to a more recent version of the database, they offer no free downloadable version. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/tree-puzzle/metadata.xml b/sci-biology/tree-puzzle/metadata.xml index 4a34df848e3a..4c857e3ebaa0 100644 --- a/sci-biology/tree-puzzle/metadata.xml +++ b/sci-biology/tree-puzzle/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of @@ -25,4 +25,6 @@ Gamma distribution and by allowing invariable sites. The corresponding parameters can be inferred from the data set. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/treeviewx/metadata.xml b/sci-biology/treeviewx/metadata.xml index 8683bbc5f8f7..82767f2fe5ac 100644 --- a/sci-biology/treeviewx/metadata.xml +++ b/sci-biology/treeviewx/metadata.xml @@ -1,14 +1,16 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> TreeView X is a program for displaying phylogenetic trees on Linux and UNIX platforms. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/trf/metadata.xml b/sci-biology/trf/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/trf/metadata.xml +++ b/sci-biology/trf/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/trnascan-se/metadata.xml b/sci-biology/trnascan-se/metadata.xml index 39da31794ca8..9df3a4de4176 100644 --- a/sci-biology/trnascan-se/metadata.xml +++ b/sci-biology/trnascan-se/metadata.xml @@ -1,15 +1,17 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second. It was implemented for large-scale human genome sequence analysis, but is applicable to other DNAs as well. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/uchime/metadata.xml b/sci-biology/uchime/metadata.xml index 8e8ff4997171..a2b5d1cad276 100644 --- a/sci-biology/uchime/metadata.xml +++ b/sci-biology/uchime/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <longdescription> UCHIME is a new algorithm for detecting chimeric sequences. It was developed in collaboration with Brian Haas, Jose Carlos Clemente, Chris Quince and Rob Knight. Chimeras are commonly created during DNA sample amplification by @@ -15,4 +15,6 @@ detect chimeras using a reference database or de novo using abundance information on the assumption that chimeras are less abundant than their parents because they must have undergone fewer rounds of amplification. </longdescription> -</pkgmetadata> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml index 042f7b949ba9..858b2b6747a5 100644 --- a/sci-biology/ucsc-genome-browser/metadata.xml +++ b/sci-biology/ucsc-genome-browser/metadata.xml @@ -1,11 +1,13 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="server">Install genome browser Web application. If this flag is off, only libraries and utilities from the suite are installed.</flag> - </use> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <use> + <flag name="server">Install genome browser Web application. If this flag is off, only libraries and utilities from the suite are installed.</flag> + </use> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/unafold/metadata.xml b/sci-biology/unafold/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/unafold/metadata.xml +++ b/sci-biology/unafold/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/update-blastdb/metadata.xml b/sci-biology/update-blastdb/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/update-blastdb/metadata.xml +++ b/sci-biology/update-blastdb/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/vcftools/metadata.xml b/sci-biology/vcftools/metadata.xml index 6c22d19200ae..fbdef0e50f2d 100644 --- a/sci-biology/vcftools/metadata.xml +++ b/sci-biology/vcftools/metadata.xml @@ -1,12 +1,13 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">vcftools</remote-id> - <remote-id type="github">vcftools/vcftools</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">vcftools</remote-id> + <remote-id type="github">vcftools/vcftools</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/velvet/metadata.xml b/sci-biology/velvet/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/velvet/metadata.xml +++ b/sci-biology/velvet/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml index fa8a259ff764..e6058d80c1dd 100644 --- a/sci-biology/wgs-assembler/metadata.xml +++ b/sci-biology/wgs-assembler/metadata.xml @@ -1,11 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">wgs-assembler</remote-id> - </upstream> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">wgs-assembler</remote-id> + </upstream> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/wise/metadata.xml b/sci-biology/wise/metadata.xml index 959160fe46b1..df75f9d83fc3 100644 --- a/sci-biology/wise/metadata.xml +++ b/sci-biology/wise/metadata.xml @@ -1,8 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file diff --git a/sci-biology/yass/metadata.xml b/sci-biology/yass/metadata.xml index 67dfef524416..c61416517138 100644 --- a/sci-biology/yass/metadata.xml +++ b/sci-biology/yass/metadata.xml @@ -1,12 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://liguros.gitlab.io/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="dmalloc">Enable debugging with the dmalloc library</flag> - <flag name="lowmem">Build for environments with low amounts of memory</flag> - </use> -</pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + + <use> + <flag name="dmalloc">Enable debugging with the dmalloc library</flag> + <flag name="lowmem">Build for environments with low amounts of memory</flag> + </use> + <origin>gentoo-staging</origin> +</pkgmetadata>
\ No newline at end of file |