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authorLiguros - Gitlab CI/CD [develop] <gitlab@liguros.net>2025-10-08 13:17:55 +0000
committerLiguros - Gitlab CI/CD [develop] <gitlab@liguros.net>2025-10-08 13:17:55 +0000
commit516d9c888c5095d1387c0451a93f0aa743a7040b (patch)
treedd9b5fbcd2572594de2bd53e769e4a692c380f34 /sci-biology
parentcaa89eacab99586878d969b5f30bd4afd8e0b3f3 (diff)
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Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/augustus/augustus-3.5.0.ebuild2
-rw-r--r--sci-biology/bcftools/bcftools-1.19.ebuild2
-rw-r--r--sci-biology/bcftools/bcftools-1.20.ebuild2
-rw-r--r--sci-biology/bcftools/bcftools-1.21.ebuild2
-rw-r--r--sci-biology/bcftools/bcftools-1.22.ebuild2
-rw-r--r--sci-biology/bedtools/bedtools-2.31.1.ebuild2
-rw-r--r--sci-biology/biopython/biopython-1.85.ebuild2
-rw-r--r--sci-biology/bowtie/bowtie-2.5.1.ebuild2
-rw-r--r--sci-biology/cytoscape-bin/Manifest1
-rw-r--r--sci-biology/cytoscape-bin/cytoscape-bin-3.10.4.ebuild40
-rw-r--r--sci-biology/jalview-bin/Manifest3
-rw-r--r--sci-biology/jalview-bin/jalview-bin-2.11.5.0.ebuild34
-rw-r--r--sci-biology/pysam/pysam-0.23.0.ebuild2
-rw-r--r--sci-biology/pysam/pysam-0.23.3.ebuild2
-rw-r--r--sci-biology/pysam/pysam-9999.ebuild2
15 files changed, 87 insertions, 13 deletions
diff --git a/sci-biology/augustus/augustus-3.5.0.ebuild b/sci-biology/augustus/augustus-3.5.0.ebuild
index 11106173dd80..bb81f7901644 100644
--- a/sci-biology/augustus/augustus-3.5.0.ebuild
+++ b/sci-biology/augustus/augustus-3.5.0.ebuild
@@ -6,7 +6,7 @@ EAPI=8
DOCS_BUILDER="doxygen"
DOCS_CONFIG_NAME="doxygen.conf"
-PYTHON_COMPAT=( python3_{9,10,11,12,13} )
+PYTHON_COMPAT=( python3_{9,10,11,12,13,14} )
inherit docs python-any-r1 toolchain-funcs
diff --git a/sci-biology/bcftools/bcftools-1.19.ebuild b/sci-biology/bcftools/bcftools-1.19.ebuild
index 20f2730a55da..943b3b69b698 100644
--- a/sci-biology/bcftools/bcftools-1.19.ebuild
+++ b/sci-biology/bcftools/bcftools-1.19.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{9,10,11,12,13} )
+PYTHON_COMPAT=( python3_{9,10,11,12,13,14} )
inherit python-single-r1
diff --git a/sci-biology/bcftools/bcftools-1.20.ebuild b/sci-biology/bcftools/bcftools-1.20.ebuild
index 20f2730a55da..943b3b69b698 100644
--- a/sci-biology/bcftools/bcftools-1.20.ebuild
+++ b/sci-biology/bcftools/bcftools-1.20.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{9,10,11,12,13} )
+PYTHON_COMPAT=( python3_{9,10,11,12,13,14} )
inherit python-single-r1
diff --git a/sci-biology/bcftools/bcftools-1.21.ebuild b/sci-biology/bcftools/bcftools-1.21.ebuild
index 0552c4cd4528..0b06b735d4a8 100644
--- a/sci-biology/bcftools/bcftools-1.21.ebuild
+++ b/sci-biology/bcftools/bcftools-1.21.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{9,10,11,12,13} )
+PYTHON_COMPAT=( python3_{9,10,11,12,13,14} )
inherit python-single-r1
diff --git a/sci-biology/bcftools/bcftools-1.22.ebuild b/sci-biology/bcftools/bcftools-1.22.ebuild
index 0552c4cd4528..0b06b735d4a8 100644
--- a/sci-biology/bcftools/bcftools-1.22.ebuild
+++ b/sci-biology/bcftools/bcftools-1.22.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{9,10,11,12,13} )
+PYTHON_COMPAT=( python3_{9,10,11,12,13,14} )
inherit python-single-r1
diff --git a/sci-biology/bedtools/bedtools-2.31.1.ebuild b/sci-biology/bedtools/bedtools-2.31.1.ebuild
index 60febc1964f7..a2592a9ca6a0 100644
--- a/sci-biology/bedtools/bedtools-2.31.1.ebuild
+++ b/sci-biology/bedtools/bedtools-2.31.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{9,10,11,12,13} )
+PYTHON_COMPAT=( python3_{9,10,11,12,13,14} )
inherit python-any-r1 toolchain-funcs
diff --git a/sci-biology/biopython/biopython-1.85.ebuild b/sci-biology/biopython/biopython-1.85.ebuild
index 809e0095ddbc..94991560fc63 100644
--- a/sci-biology/biopython/biopython-1.85.ebuild
+++ b/sci-biology/biopython/biopython-1.85.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{9,10,11,12,13} )
+PYTHON_COMPAT=( python3_{9,10,11,12,13,14} )
DISTUTILS_USE_PEP517="setuptools"
DISTUTILS_EXT=1
diff --git a/sci-biology/bowtie/bowtie-2.5.1.ebuild b/sci-biology/bowtie/bowtie-2.5.1.ebuild
index 4a7aa9da21e9..88be080955cd 100644
--- a/sci-biology/bowtie/bowtie-2.5.1.ebuild
+++ b/sci-biology/bowtie/bowtie-2.5.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{9,10,11,12,13} )
+PYTHON_COMPAT=( python3_{9,10,11,12,13,14} )
inherit python-single-r1 toolchain-funcs
diff --git a/sci-biology/cytoscape-bin/Manifest b/sci-biology/cytoscape-bin/Manifest
index 8e0a5f055ca9..5348a2468b38 100644
--- a/sci-biology/cytoscape-bin/Manifest
+++ b/sci-biology/cytoscape-bin/Manifest
@@ -1 +1,2 @@
DIST cytoscape-unix-3.10.3.tar.gz 359982151 BLAKE2B 431a5abbfb736d843cfacc18ccf553f86bb068f18112ec6aa56d85db8910b56885e40f200722bbfcf294199a24d62f79243ea1d6af265684cc69b32505bae55b SHA512 44d26d4910d44c9643b3480d3ec6e0e92606337aab83c56fccc2e40798970a8b3b9861b891c4f9103e1dd37d540ce8cb2f52438d2eeeef3d8b9e63f3620b5da6
+DIST cytoscape-unix-3.10.4.tar.gz 357480347 BLAKE2B 85f25e2a3950bd9c60721b354c0fe6b00aefc9239ec6073c1ae797677f584e9f36501a2b822a2c48e788e649955fa79384984d1cf9c79eb7189cd5124c23cd65 SHA512 36948acca38a465dedc0b2fc6063f1c1a9bdadc6d378970c21fd910ddcfc436ecc246ba685cb958b5d9f7b4505a96533da82783d91500d6fe788cbd01c958a4e
diff --git a/sci-biology/cytoscape-bin/cytoscape-bin-3.10.4.ebuild b/sci-biology/cytoscape-bin/cytoscape-bin-3.10.4.ebuild
new file mode 100644
index 000000000000..e259d4684eca
--- /dev/null
+++ b/sci-biology/cytoscape-bin/cytoscape-bin-3.10.4.ebuild
@@ -0,0 +1,40 @@
+# Copyright 2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI="8"
+
+inherit desktop java-pkg-2
+
+DESCRIPTION="A visualization platform for molecular interaction networks"
+HOMEPAGE="https://www.cytoscape.org/"
+SRC_URI="https://github.com/cytoscape/cytoscape/releases/download/${PV}/cytoscape-unix-${PV}.tar.gz"
+
+S="${WORKDIR}"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+RDEPEND="virtual/jdk:17"
+
+src_install() {
+ MY_PN="cytoscape"
+ MYW="${WORKDIR}/${MY_PN}-unix-${PV}"
+
+ insinto "/opt/${MY_PN}"
+ doins -r ${MYW}/apps
+ doins -r ${MYW}/framework
+ doins -r ${MYW}/sampleData
+
+ cd ${MYW}
+ sh gen_vmoptions.sh
+ doins Cytoscape.vmoptions
+ exeinto "/opt/${MY_PN}"
+ doexe "${MYW}/${MY_PN}.sh"
+ dosym "${EPREFIX}/opt/${MY_PN}/${MY_PN}.sh" "${EPREFIX}/opt/bin/${MY_PN}"
+
+ exeinto "/opt/${MY_PN}/framework/bin"
+ doexe framework/bin/karaf
+
+ newicon framework/cytoscape_logo_512.png cytoscape_logo.png
+ make_desktop_entry ${MY_PN} CytoScape cytoscape_logo Science
+}
diff --git a/sci-biology/jalview-bin/Manifest b/sci-biology/jalview-bin/Manifest
index ef499eb8d1ed..55096c91aa76 100644
--- a/sci-biology/jalview-bin/Manifest
+++ b/sci-biology/jalview-bin/Manifest
@@ -1,3 +1,2 @@
DIST jalview-all-2.11.4.1-j1.8.jar 50779463 BLAKE2B 847bd10f15be7a2f7ea6e50527c93037ceb07340cf1d830bf723fd499989be20a846f55fb3a04a9d59333a7a20fc336014343f502eec10bb28543c277d0b9660 SHA512 4057ac4dcb0c448f861c9fabc945dd4b77d90c5b00dda500ca73d0ea0cb476e248b93621951569586c04ea38146df8b6f3b2ad7282d63ea97e4504a267ff8663
-EBUILD jalview-bin-2.11.4.1.ebuild 780 BLAKE2B d345687df977fe683ba2da52de5a538badcc1e44469a7605f6844681c97476bb3219f7635fa72f566ce3020fff9857d1a98956c8923f498c8b404ab88587ef03 SHA512 f8a5b437a01deeae73829b1aa07c2427eb830d7e543555df776a0cd9ec10768f65ca545bac91e98bab87ec975377428f2c3b7ced606a0a96562b6e9e5d8daaa0
-MISC metadata.xml 265 BLAKE2B 23ab3b0e6c59e3f14193de28575df93c2369c3183428ad688b41c5e5aa5b4281fcbcfb802c2043cfc02704c1dc893d7cdd3308fb8ac024b4646bbc7949850f49 SHA512 6d87379308fcb616b68a8357dda5491cdfa467430af98966df579f1c96d0c8679fdffb1911d4f7fcfa82ce0e6dc408515a95d343bdf89303e0d368b5f200c986
+DIST jalview-all-2.11.5.0-j1.8.jar 51218981 BLAKE2B 7f5feee00f0c2ecdc36cb44a5b5e30378242634720afe73818e6d07923b2557195393a211d6a0992f00fc5a20a773a6183b92d6a17787e8346e7d19ad84586cb SHA512 11aa898602bebd2c39a9f5ae404edfde71e7ee077c81f7494a932f824d405f044af4451903e3b22460e4ef910c17b04330704d850e830e991e2a0ecd47ca7942
diff --git a/sci-biology/jalview-bin/jalview-bin-2.11.5.0.ebuild b/sci-biology/jalview-bin/jalview-bin-2.11.5.0.ebuild
new file mode 100644
index 000000000000..1fde572cf704
--- /dev/null
+++ b/sci-biology/jalview-bin/jalview-bin-2.11.5.0.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+JAVA_PKG_WANT_TARGET=1.8
+
+inherit desktop java-pkg-2
+
+DESCRIPTION="Editor of multiple sequence alignments."
+HOMEPAGE="https://www.jalview.org/"
+SRC_URI="https://www.jalview.org/getdown/release/jalview-all-${PV}-j1.8.jar"
+
+S="${WORKDIR}"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="app-arch/unzip"
+
+RDEPEND="virtual/jre:1.8"
+
+src_unpack() {
+ cp -v "${DISTDIR}/${A}" . || die
+ unzip -u ${A} images/jalview_logo-48.png || die
+}
+
+src_install() {
+ java-pkg_newjar "jalview-all-${PV}-j1.8.jar"
+ java-pkg_dolauncher "${PN}" --jar "${PN}.jar"
+ newicon images/jalview_logo-48.png jalview_logo_48.png
+ make_desktop_entry "${PN}" JalView jalview_logo_48 Science
+}
diff --git a/sci-biology/pysam/pysam-0.23.0.ebuild b/sci-biology/pysam/pysam-0.23.0.ebuild
index f907aa777593..b19a38059503 100644
--- a/sci-biology/pysam/pysam-0.23.0.ebuild
+++ b/sci-biology/pysam/pysam-0.23.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_EXT=1
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{9,10,11,12,13} )
+PYTHON_COMPAT=( python3_{9,10,11,12,13,14} )
inherit distutils-r1
diff --git a/sci-biology/pysam/pysam-0.23.3.ebuild b/sci-biology/pysam/pysam-0.23.3.ebuild
index 0b97b4f5ec3a..6dee617835cc 100644
--- a/sci-biology/pysam/pysam-0.23.3.ebuild
+++ b/sci-biology/pysam/pysam-0.23.3.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_EXT=1
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{9,10,11,12,13} )
+PYTHON_COMPAT=( python3_{9,10,11,12,13,14} )
inherit distutils-r1
diff --git a/sci-biology/pysam/pysam-9999.ebuild b/sci-biology/pysam/pysam-9999.ebuild
index 0fc88d632a55..dd86ad44b357 100644
--- a/sci-biology/pysam/pysam-9999.ebuild
+++ b/sci-biology/pysam/pysam-9999.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_EXT=1
DISTUTILS_USE_PEP517=setuptools
-PYTHON_COMPAT=( python3_{9,10,11,12,13} )
+PYTHON_COMPAT=( python3_{9,10,11,12,13,14} )
inherit distutils-r1
generated by cgit v1.3.1 (git 2.54.0) at 2026-06-01 13:40:03 +0000