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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-02-20 12:59:55 +0100 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-02-20 12:59:55 +0100 |
| commit | 8be5fc83dfffd37f2b607cfcbe6b17be01745594 (patch) | |
| tree | 6fba9dc0277912f51318986065ad3e11c58a01ed | |
| parent | sci-biology/tablet: do not zap jar files as we do not have a package for them... (diff) | |
| download | sci-8be5fc83dfffd37f2b607cfcbe6b17be01745594.tar.gz sci-8be5fc83dfffd37f2b607cfcbe6b17be01745594.tar.bz2 sci-8be5fc83dfffd37f2b607cfcbe6b17be01745594.zip | |
sci-biology/tablet-bin: do not zap bundled jar files as we do not have a package for them in Gentoo
Maybe except picard.jar while upstream uses picard-1.113 in tablet-1.16.09.06.
We should be around 2.0.3 with sci-biology/picard-9999 as of now.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
| -rw-r--r-- | sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild | 11 |
1 files changed, 11 insertions, 0 deletions
diff --git a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild index 4231c9411..6fc765e54 100644 --- a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild +++ b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild @@ -40,6 +40,8 @@ DEPEND="${PYTHON_DEPS} RDEPEND="${DEPEND} >=virtual/jre-1.8" # contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar +# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not sci-biology/samtools either +# replacing picard.jar with a symlink to picard.jar from sci-biology.picard does not help either S="${WORKDIR}" @@ -90,6 +92,15 @@ src_install() { rm -rf "${ED}"/opt/Tablet/jre "${ED}"/opt/Tablet/.install4j || die + # zap bundled jars + # do not zap even picard.jar because tablet does not start then with an error: + # java.lang.NoClassDefFoundError: net/sf/samtools/SAMReadGroupRecord + # not even a symlink to "${EPREFIX}"/usr/share/picard/lib/picard.jar helps + # + # for f in picard.jar; do + # rm -f "${ED}"/opt/Tablet/lib/"$f" || die + # done + # 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: |