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

[Nicolas Bock]

commit:     b1b9d3a6a59a5af4c81e7b74b655d07bc62757e9
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 28 14:06:16 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Mon Mar 31 15:27:34 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b1b9d3a6

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 <mmokrejs@×××××××××××××××.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>mmokrejs@×××××××××××××××.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
+}