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 <[email protected]> + +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 <[email protected]> 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 +}
