commit: d75c95fa5ed4db055774aff6fe3d584656076d92
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 28 14:06:16 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 28 14:06:16 2014 +0000
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d75c95fa
sci-biology/tablet: skeleton for a new package eventually to replace current
tablet-bin package
Package-Manager: portage-2.2.7
---
sci-biology/tablet/ChangeLog | 12 ++++
sci-biology/tablet/files/response.varfile | 11 +++
sci-biology/tablet/metadata.xml | 9 +++
sci-biology/tablet/tablet-1.13.12.17.ebuild | 90 +++++++++++++++++++++++++
sci-biology/tablet/tablet-9999.ebuild | 100 ++++++++++++++++++++++++++++
5 files changed, 222 insertions(+)
diff --git a/sci-biology/tablet/ChangeLog b/sci-biology/tablet/ChangeLog
new file mode 100644
index 0000000..0080ef2
--- /dev/null
+++ b/sci-biology/tablet/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/tablet
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*tablet-1.13.12.17 (28 Mar 2014)
+*tablet-9999 (28 Mar 2014)
+
+ 28 Mar 2014; Martin Mokrejs <mmokr...@fold.natur.cuni.cz>
+ +files/response.varfile, +metadata.xml, +tablet-1.13.12.17.ebuild,
+ +tablet-9999.ebuild:
+ sci-biology/tablet: skeleton for a new package eventually to replace current
+ tablet-bin package
diff --git a/sci-biology/tablet/files/response.varfile
b/sci-biology/tablet/files/response.varfile
new file mode 100644
index 0000000..cfa2e68
--- /dev/null
+++ b/sci-biology/tablet/files/response.varfile
@@ -0,0 +1,11 @@
+#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/metadata.xml b/sci-biology/tablet/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/tablet/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokr...@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/tablet/tablet-1.13.12.17.ebuild
b/sci-biology/tablet/tablet-1.13.12.17.ebuild
new file mode 100644
index 0000000..112709b
--- /dev/null
+++ b/sci-biology/tablet/tablet-1.13.12.17.ebuild
@@ -0,0 +1,90 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit java-pkg-2 python-r1
+
+DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
+HOMEPAGE="http://bioinf.scri.ac.uk/tablet/";
+SRC_URI="
+ x86? (
http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators
_).sh -> ${P}.sh )
+ amd64? (
http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators
_).sh -> ${P}.sh )
+ http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py";
+
+# Upstream says regarding source code unavailability:
+# Tablet uses a modified version of the BSD License which has been edited to
+# remove references to distribution and use in source forms. This means that
+# we are happy for you to distribute and use Tablet however you please, but we
+# do not (yet) want to make the source code publicly available.
+
+# The licence file itself is in the installer, and ends up on disk after
+# installation at /opt/Tablet/docs/tablet.html
+# The original BSD licence was modified to remove references to distribution
+# and use in source forms, because we cannot make the source code available
+# for Tablet.
+
+LICENSE="Tablet"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}"
+RDEPEND="${DEPEND}
+ virtual/jre"
+
+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 $HOME which is inside our sanbox
+ # directory area. We force -Duser.home . It seems also
-Dinstall4j.userHome
+ # could be done based on the figure shown at
http://resources.ej-technologies.com/install4j/help/doc/
+ sed \
+ -e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\"
-Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \
+ -i "${WORKDIR}"/${P}.sh || die
+ 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 || die
+
+ python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
+
+ echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
+ doenvd 99Tablet || die
+}
diff --git a/sci-biology/tablet/tablet-9999.ebuild
b/sci-biology/tablet/tablet-9999.ebuild
new file mode 100644
index 0000000..40472c7
--- /dev/null
+++ b/sci-biology/tablet/tablet-9999.ebuild
@@ -0,0 +1,100 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit java-pkg-2 java-ant-2 python-r1 eutils
+
+[ "$PV" == "9999" ] && inherit subversion
+
+DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
+HOMEPAGE="http://bioinf.scri.ac.uk/tablet/";
+if [ "$PV" == "9999" ]; then
+ ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/";
+ KEYWORDS=""
+else
+ ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}";
+ KEYWORDS=""
+fi
+
+#SRC_URI="
+# x86? (
http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators
_).sh -> ${P}.sh )
+# amd64? (
http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators
_).sh -> ${P}.sh )
+# http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py";
+
+# Upstream says regarding source code unavailability:
+# Tablet uses a modified version of the BSD License which has been edited to
+# remove references to distribution and use in source forms. This means that
+# we are happy for you to distribute and use Tablet however you please, but we
+# do not (yet) want to make the source code publicly available.
+
+# The licence file itself is in the installer, and ends up on disk after
+# installation at /opt/Tablet/docs/tablet.html
+# The original BSD licence was modified to remove references to distribution
+# and use in source forms, because we cannot make the source code available
+# for Tablet.
+
+LICENSE="Tablet"
+SLOT="0"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}
+ virtual/jdk"
+RDEPEND="${DEPEND}
+ virtual/jre"
+
+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 $HOME which is inside our sanbox
+ # directory area. We force -Duser.home . It seems also
-Dinstall4j.userHome
+ # could be done based on the figure shown at
http://resources.ej-technologies.com/install4j/help/doc/
+ sed \
+ -e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\"
-Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \
+ -i "${WORKDIR}"/${P}.sh || die
+ 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 || die
+
+ python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
+
+ echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
+ doenvd 99Tablet || die
+}
