commit: f27be8844aa92e71587cdc83eb613a73eb73308f
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Feb 20 11:58:47 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Feb 20 11:58:47 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f27be884
sci-biology/tablet: do not zap 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
sci-biology/tablet/tablet-1.15.09.01.ebuild | 21 +++++++++++----------
sci-biology/tablet/tablet-1.16.09.06.ebuild | 13 ++++++++-----
sci-biology/tablet/tablet-9999.ebuild | 13 ++++++++-----
3 files changed, 27 insertions(+), 20 deletions(-)
diff --git a/sci-biology/tablet/tablet-1.15.09.01.ebuild
b/sci-biology/tablet/tablet-1.15.09.01.ebuild
index 2d30b71bb..17f7a5365 100644
--- a/sci-biology/tablet/tablet-1.15.09.01.ebuild
+++ b/sci-biology/tablet/tablet-1.15.09.01.ebuild
@@ -30,21 +30,22 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
>=virtual/jdk-1.8:*"
RDEPEND="${PYTHON_DEPS}
- >=virtual/jre-1.8:*
- sci-biology/samtools
- sci-biology/picard
- dev-db/sqlite:3"
+ >=virtual/jre-1.8:*"
+# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
+# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not
sci-biology/samtools either
+# replacing picard.jar with a symlink to picard.jar from sci-biology.picard
does not help either
S="${WORKDIR}"
src_install() {
- cd lib || die
- java-pkg_dojar tablet.jar
+ java-pkg_dojar lib/tablet.jar
java-pkg_dolauncher ${PN}
- java-pkg_dojar tablet-resources.jar
- java-pkg_dojar flamingo.jar
- java-pkg_dojar scri-commons.jar
- java-pkg_dojar samtools*.jar
+ java-pkg_dojar lib/tablet-resources.jar
+ java-pkg_dojar lib/flamingo.jar
+ java-pkg_dojar lib/scri-commons.jar
+ java-pkg_dojar lib/samtools*.jar
+ java-pkg_dojar lib/picard*.jar
+ java-pkg_dojar lib/sqlite-jdbc*.jar
echo "PATH=${EPREFIX}/usr/share/${PN}/" > 99Tablet
doenvd 99Tablet
diff --git a/sci-biology/tablet/tablet-1.16.09.06.ebuild
b/sci-biology/tablet/tablet-1.16.09.06.ebuild
index c4be1406f..77f14a00f 100644
--- a/sci-biology/tablet/tablet-1.16.09.06.ebuild
+++ b/sci-biology/tablet/tablet-1.16.09.06.ebuild
@@ -30,19 +30,22 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
>=virtual/jdk-1.8:*"
RDEPEND="${PYTHON_DEPS}
- >=virtual/jre-1.8:*
- sci-biology/samtools
- sci-biology/picard
- dev-db/sqlite:3"
+ >=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}"
src_install() {
- java-pkg_dojar lib/tablet-resources.jar
java-pkg_dojar lib/tablet.jar
+ java-pkg_dolauncher ${PN}
+ java-pkg_dojar lib/tablet-resources.jar
java-pkg_dojar lib/flamingo.jar
java-pkg_dojar lib/scri-commons.jar
java-pkg_dojar lib/samtools*.jar
+ java-pkg_dojar lib/picard*.jar # is picard-1.113 in tablet-1.16.09.06
+ java-pkg_dojar lib/sqlite-jdbc*.jar
echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
doenvd 99Tablet
diff --git a/sci-biology/tablet/tablet-9999.ebuild
b/sci-biology/tablet/tablet-9999.ebuild
index f5846c8ef..f137ea9ad 100644
--- a/sci-biology/tablet/tablet-9999.ebuild
+++ b/sci-biology/tablet/tablet-9999.ebuild
@@ -30,19 +30,22 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
>=virtual/jdk-1.8:*"
RDEPEND="${PYTHON_DEPS}
- >=virtual/jre-1.8:*
- sci-biology/samtools
- sci-biology/picard
- dev-db/sqlite:3"
+ >=virtual/jre-1.8:*"
+# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
+# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not
sci-biology/samtools either
+# replacing picard.jar with a symlink to picard.jar from sci-biology.picard
does not help either
S="${WORKDIR}"
src_install() {
- java-pkg_dojar lib/tablet-resources.jar
java-pkg_dojar lib/tablet.jar
+ java-pkg_dolauncher ${PN}
+ java-pkg_dojar lib/tablet-resources.jar
java-pkg_dojar lib/flamingo.jar
java-pkg_dojar lib/scri-commons.jar
java-pkg_dojar lib/samtools*.jar
+ java-pkg_dojar lib/picard*.jar
+ java-pkg_dojar lib/sqlite-jdbc*.jar
echo "PATH=${EPREFIX}/usr/share/${PN}" > 99Tablet
doenvd 99Tablet
