[gentoo-commits] proj/sci:master commit in: sci-biology/tablet/

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

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