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commit: 520a2dd61f2a9b4716d34a975cd43dbefba6c41d |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Wed Jul 2 22:39:35 2014 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Wed Jul 2 22:39:35 2014 +0000 |
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URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=520a2dd6 |
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|
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sci-biology/tablet: cleaned up the ebuilds, they compile and install but the bundled samtools-*.jar is not found; updated the license |
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|
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Package-Manager: portage-2.2.7 |
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|
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--- |
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sci-biology/tablet/ChangeLog | 8 +++ |
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sci-biology/tablet/tablet-1.13.12.17.ebuild | 85 ++++++++--------------------- |
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sci-biology/tablet/tablet-1.14.04.10.ebuild | 51 +++++++++++++++++ |
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sci-biology/tablet/tablet-9999.ebuild | 77 +++++--------------------- |
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4 files changed, 96 insertions(+), 125 deletions(-) |
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|
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diff --git a/sci-biology/tablet/ChangeLog b/sci-biology/tablet/ChangeLog |
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index 0080ef2..0cca8d8 100644 |
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--- a/sci-biology/tablet/ChangeLog |
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+++ b/sci-biology/tablet/ChangeLog |
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@@ -2,6 +2,14 @@ |
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# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 |
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# $Header: $ |
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|
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+*tablet-1.14.04.10 (02 Jul 2014) |
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+ |
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+ 02 Jul 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
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+ +tablet-1.14.04.10.ebuild, -Manifest, tablet-1.13.12.17.ebuild, |
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+ tablet-9999.ebuild: |
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+ sci-biology/tablet: cleaned up the ebuilds, they compile and install but the |
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+ bundled samtools-*.jar is not found |
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+ |
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*tablet-1.13.12.17 (28 Mar 2014) |
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*tablet-9999 (28 Mar 2014) |
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|
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|
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diff --git a/sci-biology/tablet/tablet-1.13.12.17.ebuild b/sci-biology/tablet/tablet-1.13.12.17.ebuild |
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index 112709b..1940cb9 100644 |
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--- a/sci-biology/tablet/tablet-1.13.12.17.ebuild |
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+++ b/sci-biology/tablet/tablet-1.13.12.17.ebuild |
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@@ -6,84 +6,45 @@ EAPI=5 |
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|
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PYTHON_COMPAT=( python{2_6,2_7} ) |
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|
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-inherit java-pkg-2 python-r1 |
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+inherit java-pkg-2 java-ant-2 python-r1 |
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+ |
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+# [ "$PV" == "9999" ] && inherit subversion |
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+inherit subversion |
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|
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DESCRIPTION="Viewer of next generation sequence assemblies and alignments." |
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HOMEPAGE="http://bioinf.scri.ac.uk/tablet/" |
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-SRC_URI=" |
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- x86? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh ) |
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- amd64? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators _).sh -> ${P}.sh ) |
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- http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py" |
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- |
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-# Upstream says regarding source code unavailability: |
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-# Tablet uses a modified version of the BSD License which has been edited to |
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-# remove references to distribution and use in source forms. This means that |
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-# we are happy for you to distribute and use Tablet however you please, but we |
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-# do not (yet) want to make the source code publicly available. |
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- |
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-# The licence file itself is in the installer, and ends up on disk after |
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-# installation at /opt/Tablet/docs/tablet.html |
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-# The original BSD licence was modified to remove references to distribution |
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-# and use in source forms, because we cannot make the source code available |
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-# for Tablet. |
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+if [ "$PV" == "9999" ]; then |
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+ ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/" |
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+ KEYWORDS="" |
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+else |
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+ ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}" |
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+ KEYWORDS="" |
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+fi |
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|
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LICENSE="Tablet" |
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SLOT="0" |
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-KEYWORDS="" |
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IUSE="" |
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|
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REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
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|
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-DEPEND="${PYTHON_DEPS}" |
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+DEPEND="${PYTHON_DEPS} |
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+ >=virtual/jdk-1.7" |
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RDEPEND="${DEPEND} |
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- virtual/jre" |
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+ >=virtual/jre-1.7 |
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+ sci-biology/samtools |
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+ sci-biology/picard |
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+ dev-db/sqlite" |
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|
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S="${WORKDIR}" |
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|
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-src_unpack() { |
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- local file |
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- for file in ${A}; do |
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- cp "${DISTDIR}"/${file} "${WORKDIR}" || die |
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- done |
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-} |
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- |
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src_install() { |
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- # In theory it seems this binary package could be installed through ant |
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- # instead of the install4j package which is not easy to be forced |
108 |
- # non-interactive. The below approach via install4j is not ideal but works. |
109 |
- sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile > "${WORKDIR}"/response.varfile || die "sed failed" |
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- |
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- # the intallation script somehow does not pickup |
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- # -varfile="${DISTDIR}"/response.varfile from the commandline and therefore |
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- # we place the file rather directly into the place where it should reside. |
114 |
- # In the file you can read details how the variables were mangled. For |
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- # example, the trick with sys.symlinkDir in the response.varfile is to |
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- # disable the installation process to symlink from /usr/local/bin/table to |
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- # /opt/Tablet/tablet. That was logged in that file with the following line: |
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- # |
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- # /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log: |
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- # Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String] |
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- # |
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- # The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile |
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- dodir /opt/Tablet/.install4j |
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- cat "${WORKDIR}"/response.varfile > "${ED}"/opt/Tablet/.install4j/response.varfile || die |
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- |
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- # make sure we force java to point a to $HOME which is inside our sanbox |
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- # directory area. We force -Duser.home . It seems also -Dinstall4j.userHome |
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- # could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/ |
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- sed \ |
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- -e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \ |
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- -i "${WORKDIR}"/${P}.sh || die |
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- sh \ |
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- "${WORKDIR}"/${P}.sh \ |
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- -q -overwrite \ |
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- -varfile="${DISTDIR}"/response.varfile \ |
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- --destination="${ED}"/opt/Tablet \ |
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- -dir "${ED}"/opt/Tablet || die |
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- |
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- rm -rf "${ED}"/opt/Tablet/jre || die |
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+ java-pkg_dojar lib/tablet-resources.jar || die |
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+ java-pkg_dojar lib/tablet.jar || die |
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+ java-pkg_dojar lib/flamingo.jar || die |
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+ java-pkg_dojar lib/scri-commons.jar || die |
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+ java-pkg_dojar lib/samtools*.jar || die |
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|
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- python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py |
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+ dobin www/additional/coveragestats.py |
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|
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echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet |
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doenvd 99Tablet || die |
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|
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diff --git a/sci-biology/tablet/tablet-1.14.04.10.ebuild b/sci-biology/tablet/tablet-1.14.04.10.ebuild |
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new file mode 100644 |
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index 0000000..1940cb9 |
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--- /dev/null |
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+++ b/sci-biology/tablet/tablet-1.14.04.10.ebuild |
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@@ -0,0 +1,51 @@ |
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+# Copyright 1999-2014 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Header: $ |
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+ |
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+EAPI=5 |
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+ |
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+PYTHON_COMPAT=( python{2_6,2_7} ) |
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+ |
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+inherit java-pkg-2 java-ant-2 python-r1 |
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+ |
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+# [ "$PV" == "9999" ] && inherit subversion |
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+inherit subversion |
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+ |
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+DESCRIPTION="Viewer of next generation sequence assemblies and alignments." |
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+HOMEPAGE="http://bioinf.scri.ac.uk/tablet/" |
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+if [ "$PV" == "9999" ]; then |
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+ ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/" |
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+ KEYWORDS="" |
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+else |
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+ ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}" |
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+ KEYWORDS="" |
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+fi |
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+ |
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+LICENSE="Tablet" |
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+SLOT="0" |
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+IUSE="" |
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+ |
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+REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
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+ |
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+DEPEND="${PYTHON_DEPS} |
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+ >=virtual/jdk-1.7" |
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+RDEPEND="${DEPEND} |
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+ >=virtual/jre-1.7 |
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+ sci-biology/samtools |
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+ sci-biology/picard |
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+ dev-db/sqlite" |
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+ |
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+S="${WORKDIR}" |
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+ |
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+src_install() { |
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+ java-pkg_dojar lib/tablet-resources.jar || die |
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+ java-pkg_dojar lib/tablet.jar || die |
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+ java-pkg_dojar lib/flamingo.jar || die |
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+ java-pkg_dojar lib/scri-commons.jar || die |
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+ java-pkg_dojar lib/samtools*.jar || die |
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+ |
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+ dobin www/additional/coveragestats.py |
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+ |
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+ echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet |
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+ doenvd 99Tablet || die |
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+} |
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|
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diff --git a/sci-biology/tablet/tablet-9999.ebuild b/sci-biology/tablet/tablet-9999.ebuild |
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index 40472c7..1940cb9 100644 |
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--- a/sci-biology/tablet/tablet-9999.ebuild |
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+++ b/sci-biology/tablet/tablet-9999.ebuild |
214 |
@@ -6,9 +6,10 @@ EAPI=5 |
215 |
|
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PYTHON_COMPAT=( python{2_6,2_7} ) |
217 |
|
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-inherit java-pkg-2 java-ant-2 python-r1 eutils |
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+inherit java-pkg-2 java-ant-2 python-r1 |
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|
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-[ "$PV" == "9999" ] && inherit subversion |
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+# [ "$PV" == "9999" ] && inherit subversion |
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+inherit subversion |
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|
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DESCRIPTION="Viewer of next generation sequence assemblies and alignments." |
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HOMEPAGE="http://bioinf.scri.ac.uk/tablet/" |
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@@ -20,23 +21,6 @@ else |
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KEYWORDS="" |
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fi |
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|
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-#SRC_URI=" |
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-# x86? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh ) |
233 |
-# amd64? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators _).sh -> ${P}.sh ) |
234 |
-# http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py" |
235 |
- |
236 |
-# Upstream says regarding source code unavailability: |
237 |
-# Tablet uses a modified version of the BSD License which has been edited to |
238 |
-# remove references to distribution and use in source forms. This means that |
239 |
-# we are happy for you to distribute and use Tablet however you please, but we |
240 |
-# do not (yet) want to make the source code publicly available. |
241 |
- |
242 |
-# The licence file itself is in the installer, and ends up on disk after |
243 |
-# installation at /opt/Tablet/docs/tablet.html |
244 |
-# The original BSD licence was modified to remove references to distribution |
245 |
-# and use in source forms, because we cannot make the source code available |
246 |
-# for Tablet. |
247 |
- |
248 |
LICENSE="Tablet" |
249 |
SLOT="0" |
250 |
IUSE="" |
251 |
@@ -44,56 +28,23 @@ IUSE="" |
252 |
REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
253 |
|
254 |
DEPEND="${PYTHON_DEPS} |
255 |
- virtual/jdk" |
256 |
+ >=virtual/jdk-1.7" |
257 |
RDEPEND="${DEPEND} |
258 |
- virtual/jre" |
259 |
+ >=virtual/jre-1.7 |
260 |
+ sci-biology/samtools |
261 |
+ sci-biology/picard |
262 |
+ dev-db/sqlite" |
263 |
|
264 |
S="${WORKDIR}" |
265 |
|
266 |
-src_unpack() { |
267 |
- local file |
268 |
- for file in ${A}; do |
269 |
- cp "${DISTDIR}"/${file} "${WORKDIR}" || die |
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- done |
271 |
-} |
272 |
- |
273 |
src_install() { |
274 |
- # In theory it seems this binary package could be installed through ant |
275 |
- # instead of the install4j package which is not easy to be forced |
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- # non-interactive. The below approach via install4j is not ideal but works. |
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- sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile > "${WORKDIR}"/response.varfile || die "sed failed" |
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- |
279 |
- # the intallation script somehow does not pickup |
280 |
- # -varfile="${DISTDIR}"/response.varfile from the commandline and therefore |
281 |
- # we place the file rather directly into the place where it should reside. |
282 |
- # In the file you can read details how the variables were mangled. For |
283 |
- # example, the trick with sys.symlinkDir in the response.varfile is to |
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- # disable the installation process to symlink from /usr/local/bin/table to |
285 |
- # /opt/Tablet/tablet. That was logged in that file with the following line: |
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- # |
287 |
- # /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log: |
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- # Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String] |
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- # |
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- # The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile |
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- dodir /opt/Tablet/.install4j |
292 |
- cat "${WORKDIR}"/response.varfile > "${ED}"/opt/Tablet/.install4j/response.varfile || die |
293 |
- |
294 |
- # make sure we force java to point a to $HOME which is inside our sanbox |
295 |
- # directory area. We force -Duser.home . It seems also -Dinstall4j.userHome |
296 |
- # could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/ |
297 |
- sed \ |
298 |
- -e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \ |
299 |
- -i "${WORKDIR}"/${P}.sh || die |
300 |
- sh \ |
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- "${WORKDIR}"/${P}.sh \ |
302 |
- -q -overwrite \ |
303 |
- -varfile="${DISTDIR}"/response.varfile \ |
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- --destination="${ED}"/opt/Tablet \ |
305 |
- -dir "${ED}"/opt/Tablet || die |
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- |
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- rm -rf "${ED}"/opt/Tablet/jre || die |
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+ java-pkg_dojar lib/tablet-resources.jar || die |
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+ java-pkg_dojar lib/tablet.jar || die |
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+ java-pkg_dojar lib/flamingo.jar || die |
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+ java-pkg_dojar lib/scri-commons.jar || die |
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+ java-pkg_dojar lib/samtools*.jar || die |
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|
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- python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py |
315 |
+ dobin www/additional/coveragestats.py |
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|
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echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet |
318 |
doenvd 99Tablet || die |