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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
PYTHON_COMPAT=( python2_7 )
inherit java-pkg-2 python-r1
DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
HOMEPAGE="http://ics.hutton.ac.uk/tablet/"
SRC_URI="
x86? ( http://bioinf.hutton.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh )
amd64? ( http://bioinf.hutton.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators _).sh -> ${P}.sh )
http://bioinf.hutton.ac.uk/tablet/additional/coveragestats.py"
# Upstream says regarding source code unavailability:
# Tablet uses a modified version of the BSD License which has been edited to
# remove references to distribution and use in source forms. This means that
# we are happy for you to distribute and use Tablet however you please, but we
# do not (yet) want to make the source code publicly available.
# The licence file itself is in the installer, and ends up on disk after
# installation at /opt/Tablet/docs/tablet.html
# The original BSD licence was modified to remove references to distribution
# and use in source forms, because we cannot make the source code available
# for Tablet.
LICENSE="Tablet"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
REQUIRED_USE="${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
}
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