[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/files/, sci-biology/tablet-bin/

[Andrew Ammerlaan]

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>mmokrejs@×××××××××××××××.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@g.o</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
-}