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authorMartin Mokrejs <mmokrejs@gmail.com>2020-01-10 17:01:02 +0100
committerMartin Mokrejs <mmokrejs@gmail.com>2020-01-10 17:06:00 +0100
commit225240b5c35e442b575dd91b659c1b8171a88397 (patch)
treeaaf5d41c33da69b5c118fd8cc49ed6e2e9b7a51d /sci-biology
parentsci-biology/NGSEPcore: cleanup the ebuild (diff)
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sci-biology/NGSEPcore-bin: binaries from upstream
sci-biology/NGSEPplugin-bin: upstream binaries sci-biology/NGSEPplugin: add current HOMEPAGE Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/NGSEPcore-bin/Manifest4
-rw-r--r--sci-biology/NGSEPcore-bin/NGSEPcore-bin-3.3.1.ebuild37
-rw-r--r--sci-biology/NGSEPcore-bin/metadata.xml15
-rw-r--r--sci-biology/NGSEPplugin-bin/Manifest1
-rw-r--r--sci-biology/NGSEPplugin-bin/NGSEPplugin-bin-3.3.1.ebuild28
-rw-r--r--sci-biology/NGSEPplugin-bin/metadata.xml15
-rw-r--r--sci-biology/NGSEPplugin/NGSEPplugin-3.3.1.ebuild5
7 files changed, 103 insertions, 2 deletions
diff --git a/sci-biology/NGSEPcore-bin/Manifest b/sci-biology/NGSEPcore-bin/Manifest
new file mode 100644
index 000000000..b960f10df
--- /dev/null
+++ b/sci-biology/NGSEPcore-bin/Manifest
@@ -0,0 +1,4 @@
+DIST NGSEPcore-bin-3.3.1_QuickStart.txt 23701 BLAKE2B 0b3433a771e0121d4f38362f331e87c2597b7cbca4b63f26504807b2a84de2a3636e711c6bdee86c575810d6aff44996cb75663739ff5e184542f7f598f546be SHA512 d1eff40ca54a1e9bbdbda59511eb9e63ace2b001024df4119f0751b2e00dcf9219eb2eaa6407b2ccd1df71cf93d9b8e39088a59b7a6200fd966502c1b680eedd
+DIST NGSEPcore-bin-3.3.1_Tutorial.txt 17070 BLAKE2B 9af46173da8cb1b1746118d186da0794c0b9ad11d22109bdf96ed9df6d21df2495e8be3e5e75ef013a11922aa697ceb85ee280199eebbb2afadc180d3d86c0a6 SHA512 844138e0be2038d3f4656a55a8129819f08361cb6447a7fdb261b48c1f50e7aad1234079cbb01746bc7084d59c79589538883ecc0b0bb4bd8e07f61861ef80c1
+DIST NGSEPcore-bin-3.3.1_UserManual.pdf 29071950 BLAKE2B fd16b44e3668f61013772965378bf4fa604b2467839810392d26a27e1a6e52f961cecc5097728bb67d10b68556bd406ec044b439c5ad1b3e614bfc7866afed43 SHA512 6d697f6945bdecb4f30712d3ae94615c85180a53750ba92357f81bf060b3f5bec3f6d1a03115c1a3791f5bf050b115cd09fd8729d885d4ec34b10024082ebb3c
+DIST NGSEPcore_3.3.1.jar 2288599 BLAKE2B 16e1754349d312c9172b80d264e480835f9784452ed022d39931756d650971247781abee179afe9b73cef6413ab0604c7232b38c65b0ad98d0d5f60a02cc7e91 SHA512 4bb938b0b22f77703d8567f3e95b2dd1df6d56edae522521cada8b72e9cd6ac265b30c70f3c480107aa17210b9d5b8e43a14617137bb3f1333c1ce70f5cc5439
diff --git a/sci-biology/NGSEPcore-bin/NGSEPcore-bin-3.3.1.ebuild b/sci-biology/NGSEPcore-bin/NGSEPcore-bin-3.3.1.ebuild
new file mode 100644
index 000000000..8758da3ac
--- /dev/null
+++ b/sci-biology/NGSEPcore-bin/NGSEPcore-bin-3.3.1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="NGSEP (CNV and indel discovery)"
+HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home
+ https://github.com/NGSEP/NGSEPcore"
+SRC_URI="https://sourceforge.net/projects/ngsep/files/Library/NGSEPcore_3.3.1.jar
+ https://sourceforge.net/projects/ngsep/files/training/UserManualNGSEP_V330.pdf -> ${P}_UserManual.pdf
+ https://sourceforge.net/projects/ngsep/files/training/Tutorial.txt -> ${P}_Tutorial.txt
+ https://sourceforge.net/projects/ngsep/files/training/QuickStart.txt -> ${P}_QuickStart.txt"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+ dev-java/htsjdk"
+# dev-java/jsci-bin
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"
+
+src_unpack(){
+ echo
+}
+
+src_install(){
+ java-pkg_dojar "${DISTDIR}"/*.jar
+ dodoc "${DISTDIR}"/${P}_UserManual.pdf \
+ "${DISTDIR}"/${P}_Tutorial.txt \
+ "${DISTDIR}"/${P}_QuickStart.txt
+}
diff --git a/sci-biology/NGSEPcore-bin/metadata.xml b/sci-biology/NGSEPcore-bin/metadata.xml
new file mode 100644
index 000000000..642261079
--- /dev/null
+++ b/sci-biology/NGSEPcore-bin/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="sourceforge">ngsep</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/NGSEPplugin-bin/Manifest b/sci-biology/NGSEPplugin-bin/Manifest
new file mode 100644
index 000000000..32b7ad470
--- /dev/null
+++ b/sci-biology/NGSEPplugin-bin/Manifest
@@ -0,0 +1 @@
+DIST NGSEPplugin_3.3.1.201903140636.jar 4265549 BLAKE2B 016142b652f8cea94e6206d014b4f193b8b59dd277ce82d5a927f18b6826e4c702f5594c9379db5664a8b4e3ba5aac87c6e100ec1c0990c349cea3ca178d5321 SHA512 b0e008cb1fcca6925be681679f64f6dc8f4de5362d126ebce637f9ac533b7e90123d9167b73050971623cd3b512df66fbab79f1df0e4bfef0c4c9651de157844
diff --git a/sci-biology/NGSEPplugin-bin/NGSEPplugin-bin-3.3.1.ebuild b/sci-biology/NGSEPplugin-bin/NGSEPplugin-bin-3.3.1.ebuild
new file mode 100644
index 000000000..f2a452138
--- /dev/null
+++ b/sci-biology/NGSEPplugin-bin/NGSEPplugin-bin-3.3.1.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="NGSEP with Eclipse Plugin (CNV and indel discovery)"
+HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home
+ https://github.com/NGSEP/NGSEPplugin"
+SRC_URI="https://sourceforge.net/projects/ngsep/files/OnlyPlugin/NGSEPplugin_3.3.1.201903140636.jar"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+ >=virtual/jdk-1.7:*
+ sci-biology/NGSEPcore-bin"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.7:*"
+
+S="${WORKDIR}"
+
+src_install(){
+ java-pkg_dojar "${DISTDIR}"/*.jar
+}
diff --git a/sci-biology/NGSEPplugin-bin/metadata.xml b/sci-biology/NGSEPplugin-bin/metadata.xml
new file mode 100644
index 000000000..642261079
--- /dev/null
+++ b/sci-biology/NGSEPplugin-bin/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="sourceforge">ngsep</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-biology/NGSEPplugin/NGSEPplugin-3.3.1.ebuild b/sci-biology/NGSEPplugin/NGSEPplugin-3.3.1.ebuild
index ec13ffa46..736121efb 100644
--- a/sci-biology/NGSEPplugin/NGSEPplugin-3.3.1.ebuild
+++ b/sci-biology/NGSEPplugin/NGSEPplugin-3.3.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -6,7 +6,8 @@ EAPI=7
inherit java-pkg-2 java-ant-2
DESCRIPTION="NGSEP with Eclipse Plugin (CNV and indel discovery)"
-HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home"
+HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home
+ https://github.com/NGSEP/NGSEPplugin"
SRC_URI="https://sourceforge.net/projects/ngsep/files/SourceCode/NGSEPplugin_${PV}.tar.gz"
LICENSE="GPL-3"