commit: ecd3b3602cb2f9728ea08d2cd72c3d37f8373f93
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Feb 1 05:07:34 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Feb 1 05:07:34 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ecd3b360
sci-biology/tablet-bin: drop pack, py2 only
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/tablet-bin/files/response.varfile | 11 ---
sci-biology/tablet-bin/metadata.xml | 12 ---
.../tablet-bin/tablet-bin-1.20.12.24.ebuild | 105 ---------------------
3 files changed, 128 deletions(-)
diff --git a/sci-biology/tablet-bin/files/response.varfile
b/sci-biology/tablet-bin/files/response.varfile
deleted file mode 100644
index cfa2e6808..000000000
--- a/sci-biology/tablet-bin/files/response.varfile
+++ /dev/null
@@ -1,11 +0,0 @@
-#install4j response file for Tablet x.xx.xx.xx
-#Mon Jan 24 11:35:29 GMT 2011
-executeLauncherAction$Boolean=false
-sys.programGroupDisabled$Boolean=true
-# somehow, this happens: ln -s
/scratch/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/tablet
/usr/local/bin/tablet
-# # that happens because
/scratch/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/response.varfile
does not reflect our values
-sys.symlinkDir="${D}"usr/bin
-#sys.symlinkDir=/scratch/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/usr/bin
-sys.languageId=en
-sys.userHome="${D}"/../temp
-sys.installationDir="${D}"opt/Tablet
diff --git a/sci-biology/tablet-bin/metadata.xml
b/sci-biology/tablet-bin/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/tablet-bin/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="person">
- <email>[email protected]</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>[email protected]</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/tablet-bin/tablet-bin-1.20.12.24.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.20.12.24.ebuild
deleted file mode 100644
index 697ae0d36..000000000
--- a/sci-biology/tablet-bin/tablet-bin-1.20.12.24.ebuild
+++ /dev/null
@@ -1,105 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit java-pkg-2 python-r1
-
-DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
-HOMEPAGE="https://ics.hutton.ac.uk/tablet";
-SRC_URI="
- x86? (
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x86_$(ver_rs
0-3 _).sh -> ${P}.sh )
- amd64? (
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x64_$(ver_rs
0-3 _).sh -> ${P}.sh )
- https://bioinf.hutton.ac.uk/tablet/additional/coveragestats.py";
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
- app-text/dos2unix
- >=virtual/jdk-1.8:*"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.8:*"
-# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
-# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not
sci-biology/samtools either
-# replacing picard.jar with a symlink to picard.jar from sci-biology.picard
does not help either
-
-S="${WORKDIR}"
-
-src_unpack() {
- local file
- for file in ${A}; do
- cp "${DISTDIR}"/${file} "${WORKDIR}" || die
- done
-}
-
-src_install() {
- # In theory it seems this binary package could be installed through ant
- # instead of the install4j package which is not easy to be forced
- # non-interactive. The below approach via install4j is not ideal but
works.
- sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile >
"${WORKDIR}"/response.varfile || die "sed failed"
-
- # the intallation script somehow does not pickup
- # -varfile="${DISTDIR}"/response.varfile from the commandline and
therefore
- # we place the file rather directly into the place where it should
reside.
- # In the file you can read details how the variables were mangled. For
- # example, the trick with sys.symlinkDir in the response.varfile is to
- # disable the installation process to symlink from /usr/local/bin/table
to
- # /opt/Tablet/tablet. That was logged in that file with the following
line:
- #
- #
/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log:
- # Variable changed: sys.symlinkDir=/usr/local/bin[class
java.lang.String]
- #
- # The file is then left on the installed system in
"${D}"/opt/Tablet/.install4j/response.varfile
- dodir /opt/Tablet/.install4j
- cat "${WORKDIR}"/response.varfile >
"${ED}"/opt/Tablet/.install4j/response.varfile || die
-
- # make sure we force java to point a to $HOME which is inside our sanbox
- # directory area. We force -Duser.home . It seems also
-Dinstall4j.userHome
- # could be done based on the figure shown at
http://resources.ej-technologies.com/install4j/help/doc/
- if [ -z "${EPREFIX}" ]; then
- sed \
- -e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\"
-Duser.home=${TMPDIR} -Dinstall4j.jvmDir
-Djava.util.prefs.systemRoot=${TMPDIR}#" -i "${WORKDIR}"/${P}.sh || die
- else
- sed \
- -e 's#"$app_java_home/bin/java" -Dinstall4j.jvmDir#
'"${EPREFIX}""/usr/bin/java -Duser.home=${TMPDIR} -Dinstall4j.jvmDir
-Djava.util.prefs.systemRoot=${TMPDIR}#" -i "${WORKDIR}"/${P}.sh || die
- fi
- sh \
- "${WORKDIR}"/${P}.sh \
- -q -overwrite \
- -varfile="${DISTDIR}"/response.varfile \
- --destination="${ED}"/opt/Tablet \
- -dir "${ED}"/opt/Tablet || die
-
- rm -rf "${ED}"/opt/Tablet/jre "${ED}"/opt/Tablet/.install4j || die
-
- # zap bundled jars
- # do not zap even picard.jar because tablet does not start then with an
error:
- # java.lang.NoClassDefFoundError: net/sf/samtools/SAMReadGroupRecord
- # not even a symlink to "${EPREFIX}"/usr/share/picard/lib/picard.jar
helps
- #
- # for f in picard.jar; do
- # rm -f "${ED}"/opt/Tablet/lib/"$f" || die
- # done
-
- # this dies with tablet-bin-1.14.04.10 with
- # * python2_7: running python_doscript
/mnt/1TB/var/tmp/portage/sci-biology/tablet-bin-1.14.04.10/work/coveragestats.py
- # * The file has incompatible shebang:
- # * file: /usr/lib/python-exec/python2.7/coveragestats.py
- # * current shebang: #!/usr/bin/env python
- # * requested impl: python2.7
- #
- # python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
- dos2unix "${WORKDIR}"/coveragestats.py coveragestats.py || die
- insinto /opt/Tablet/utils
- doins coveragestats.py
-
- # do not use 99Tablet to avoid file collision with sci-biology/tablet
- echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet-bin
- doenvd 99Tablet-bin
-}
