commit: 520a2dd61f2a9b4716d34a975cd43dbefba6c41d Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Jul 2 22:39:35 2014 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Jul 2 22:39:35 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=520a2dd6
sci-biology/tablet: cleaned up the ebuilds, they compile and install but the bundled samtools-*.jar is not found; updated the license Package-Manager: portage-2.2.7 --- sci-biology/tablet/ChangeLog | 8 +++ sci-biology/tablet/tablet-1.13.12.17.ebuild | 85 ++++++++--------------------- sci-biology/tablet/tablet-1.14.04.10.ebuild | 51 +++++++++++++++++ sci-biology/tablet/tablet-9999.ebuild | 77 +++++--------------------- 4 files changed, 96 insertions(+), 125 deletions(-) diff --git a/sci-biology/tablet/ChangeLog b/sci-biology/tablet/ChangeLog index 0080ef2..0cca8d8 100644 --- a/sci-biology/tablet/ChangeLog +++ b/sci-biology/tablet/ChangeLog @@ -2,6 +2,14 @@ # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*tablet-1.14.04.10 (02 Jul 2014) + + 02 Jul 2014; Martin Mokrejs <[email protected]> + +tablet-1.14.04.10.ebuild, -Manifest, tablet-1.13.12.17.ebuild, + tablet-9999.ebuild: + sci-biology/tablet: cleaned up the ebuilds, they compile and install but the + bundled samtools-*.jar is not found + *tablet-1.13.12.17 (28 Mar 2014) *tablet-9999 (28 Mar 2014) diff --git a/sci-biology/tablet/tablet-1.13.12.17.ebuild b/sci-biology/tablet/tablet-1.13.12.17.ebuild index 112709b..1940cb9 100644 --- a/sci-biology/tablet/tablet-1.13.12.17.ebuild +++ b/sci-biology/tablet/tablet-1.13.12.17.ebuild @@ -6,84 +6,45 @@ EAPI=5 PYTHON_COMPAT=( python{2_6,2_7} ) -inherit java-pkg-2 python-r1 +inherit java-pkg-2 java-ant-2 python-r1 + +# [ "$PV" == "9999" ] && inherit subversion +inherit subversion DESCRIPTION="Viewer of next generation sequence assemblies and alignments." HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"; -SRC_URI=" - x86? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh ) - amd64? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators _).sh -> ${P}.sh ) - http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"; - -# Upstream says regarding source code unavailability: -# Tablet uses a modified version of the BSD License which has been edited to -# remove references to distribution and use in source forms. This means that -# we are happy for you to distribute and use Tablet however you please, but we -# do not (yet) want to make the source code publicly available. - -# The licence file itself is in the installer, and ends up on disk after -# installation at /opt/Tablet/docs/tablet.html -# The original BSD licence was modified to remove references to distribution -# and use in source forms, because we cannot make the source code available -# for Tablet. +if [ "$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/${PV}"; + KEYWORDS="" +fi LICENSE="Tablet" SLOT="0" -KEYWORDS="" IUSE="" REQUIRED_USE="${PYTHON_REQUIRED_USE}" -DEPEND="${PYTHON_DEPS}" +DEPEND="${PYTHON_DEPS} + >=virtual/jdk-1.7" RDEPEND="${DEPEND} - virtual/jre" + >=virtual/jre-1.7 + sci-biology/samtools + sci-biology/picard + dev-db/sqlite" S="${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 + java-pkg_dojar lib/tablet-resources.jar || die + java-pkg_dojar lib/tablet.jar || die + java-pkg_dojar lib/flamingo.jar || die + java-pkg_dojar lib/scri-commons.jar || die + java-pkg_dojar lib/samtools*.jar || die - python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py + dobin www/additional/coveragestats.py echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet doenvd 99Tablet || die diff --git a/sci-biology/tablet/tablet-1.14.04.10.ebuild b/sci-biology/tablet/tablet-1.14.04.10.ebuild new file mode 100644 index 0000000..1940cb9 --- /dev/null +++ b/sci-biology/tablet/tablet-1.14.04.10.ebuild @@ -0,0 +1,51 @@ +# 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 + +# [ "$PV" == "9999" ] && inherit subversion +inherit subversion + +DESCRIPTION="Viewer of next generation sequence assemblies and alignments." +HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"; +if [ "$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/${PV}"; + KEYWORDS="" +fi + +LICENSE="Tablet" +SLOT="0" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND="${PYTHON_DEPS} + >=virtual/jdk-1.7" +RDEPEND="${DEPEND} + >=virtual/jre-1.7 + sci-biology/samtools + sci-biology/picard + dev-db/sqlite" + +S="${WORKDIR}" + +src_install() { + java-pkg_dojar lib/tablet-resources.jar || die + java-pkg_dojar lib/tablet.jar || die + java-pkg_dojar lib/flamingo.jar || die + java-pkg_dojar lib/scri-commons.jar || die + java-pkg_dojar lib/samtools*.jar || die + + dobin www/additional/coveragestats.py + + echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet + doenvd 99Tablet || die +} diff --git a/sci-biology/tablet/tablet-9999.ebuild b/sci-biology/tablet/tablet-9999.ebuild index 40472c7..1940cb9 100644 --- a/sci-biology/tablet/tablet-9999.ebuild +++ b/sci-biology/tablet/tablet-9999.ebuild @@ -6,9 +6,10 @@ EAPI=5 PYTHON_COMPAT=( python{2_6,2_7} ) -inherit java-pkg-2 java-ant-2 python-r1 eutils +inherit java-pkg-2 java-ant-2 python-r1 -[ "$PV" == "9999" ] && inherit subversion +# [ "$PV" == "9999" ] && inherit subversion +inherit subversion DESCRIPTION="Viewer of next generation sequence assemblies and alignments." HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"; @@ -20,23 +21,6 @@ else 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 -> ${P}.sh ) -# http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"; - -# Upstream says regarding source code unavailability: -# Tablet uses a modified version of the BSD License which has been edited to -# remove references to distribution and use in source forms. This means that -# we are happy for you to distribute and use Tablet however you please, but we -# do not (yet) want to make the source code publicly available. - -# The licence file itself is in the installer, and ends up on disk after -# installation at /opt/Tablet/docs/tablet.html -# The original BSD licence was modified to remove references to distribution -# and use in source forms, because we cannot make the source code available -# for Tablet. - LICENSE="Tablet" SLOT="0" IUSE="" @@ -44,56 +28,23 @@ IUSE="" REQUIRED_USE="${PYTHON_REQUIRED_USE}" DEPEND="${PYTHON_DEPS} - virtual/jdk" + >=virtual/jdk-1.7" RDEPEND="${DEPEND} - virtual/jre" + >=virtual/jre-1.7 + sci-biology/samtools + sci-biology/picard + dev-db/sqlite" 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 + java-pkg_dojar lib/tablet-resources.jar || die + java-pkg_dojar lib/tablet.jar || die + java-pkg_dojar lib/flamingo.jar || die + java-pkg_dojar lib/scri-commons.jar || die + java-pkg_dojar lib/samtools*.jar || die - python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py + dobin www/additional/coveragestats.py echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet doenvd 99Tablet || die
