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

[Martin Mokrejs]

commit:     01ff3a2d6b36716aa83e749acfeb4cc09e076ba8
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jul  2 22:40:49 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jul  2 22:40:49 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=01ff3a2d

sci-biology/tablet-bin: version bump; updated the license

Package-Manager: portage-2.2.7

---
 sci-biology/tablet-bin/ChangeLog                   |  6 ++
 .../tablet-bin/tablet-bin-1.14.04.10.ebuild        | 97 ++++++++++++++++++++++
 2 files changed, 103 insertions(+)

diff --git a/sci-biology/tablet-bin/ChangeLog b/sci-biology/tablet-bin/ChangeLog
index d48473a..8b38781 100644
--- a/sci-biology/tablet-bin/ChangeLog
+++ b/sci-biology/tablet-bin/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*tablet-bin-1.14.04.10 (02 Jul 2014)
+
+  02 Jul 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  +tablet-bin-1.14.04.10.ebuild:
+  sci-biology/tablet-bin: version bump; updated the license
+
 *tablet-bin-1.13.12.17 (20 Jan 2014)
 
   20 Jan 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>

diff --git a/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild b/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild
new file mode 100644
index 0000000..1a0fdf1
--- /dev/null
+++ b/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild
@@ -0,0 +1,97 @@
+# 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 -> ${P}.sh )
+	http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
+
+# Upstream says regarding source code unavailability:
+# Tablet uses a modified version of the BSD License which has been edited to
+# remove references to distribution and use in source forms. This means that
+# we are happy for you to distribute and use Tablet however you please, but we
+# do not (yet) want to make the source code publicly available.
+
+# The licence file itself is in the installer, and ends up on disk after
+# installation at /opt/Tablet/docs/tablet.html
+# The original BSD licence was modified to remove references to distribution
+# and use in source forms, because we cannot make the source code available
+# for Tablet.
+
+LICENSE="Tablet"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+REQUIRED_USE="${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
+
+    # 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 "${WORKDIR}"/coveragestats.py
+
+	echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
+	doenvd 99Tablet || die
+}