commit: 3bd45176e875ab2b69e36a4d430dbb4b5410fb3d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov 15 20:18:48 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 15 20:18:48 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3bd45176
sci-biology/jannovar: working ebuild, although maven re-fetches 95MB of its deps
Package-Manager: portage-2.3.2
sci-biology/jannovar/jannovar-0.16.ebuild | 43 +++++++++++++++++++++++++------
1 file changed, 35 insertions(+), 8 deletions(-)
diff --git a/sci-biology/jannovar/jannovar-0.16.ebuild
b/sci-biology/jannovar/jannovar-0.16.ebuild
index c67b789..5b13048 100644
--- a/sci-biology/jannovar/jannovar-0.16.ebuild
+++ b/sci-biology/jannovar/jannovar-0.16.ebuild
@@ -16,21 +16,48 @@ SLOT="0"
KEYWORDS=""
IUSE=""
+COMMON_DEPS="
+ dev-java/commons-compress
+ dev-java/commons-io
+ dev-java/commons-jexl:*
+ dev-java/commons-logging:0
+ dev-java/commons-net
+ dev-java/guava:*
+ dev-java/hamcrest-core:*
+ dev-java/htsjdk
+ dev-java/ini4j
+ dev-java/junit:*
+ dev-java/log4j:0"
DEPEND=">=virtual/jdk-1.6
- dev-java/maven-bin:*"
-RDEPEND=">=virtual/jre-1.6"
+ dev-java/maven-bin:*
+ ${COMMON_DEPS}"
+RDEPEND=">=virtual/jre-1.6
+ ${COMMON_DEPS}"
# TODO: set a proxy because it downloads data during compile step
# http://jannovar.readthedocs.io/en/master/install.html
# see https://github.com/charite/jannovar/issues/218
+# https://maven.apache.org/settings.html#Proxies
src_compile(){
- mvn package -Dmaven.test.skip.exec=true -DskipTests=true || die
+ mvn package -Dmaven.test.skip.exec=true -DskipTests=true
-Duser.home="${HOME}" || die
}
src_install(){
- mvn install -Dmaven.test.skip.exec=true || die
- java-pkg_dojar jannovar-cli.jar
- java-pkg_dolauncher jannovar-cli --jar jannovar-cli.jar
- java-pkg_dojar jped-cli.jar
- java-pkg_dolauncher jped-cli --jar jped-cli.jar
+ # maven download 95MB from the network into
"${PORTAGE_BUILDDIR}/homedir/"
+ export M2="${HOME}"
+ mvn install -Dmaven.test.skip.exec=true -Duser.home="${HOME}" || die
+ java-pkg_dojar jannovar-cli/target/jannovar-cli-0.16.jar
+ java-pkg_dolauncher jannovar-cli --jar jannovar-cli-0.16.jar
+ java-pkg_dojar jped-cli/target/jped-cli-0.16.jar
+ java-pkg_dolauncher jped-cli --jar jped-cli-0.16.jar
+ #java-pkg_dojar jannovar-hgvs/target/jannovar-hgvs-0.16.jar
+ #java-pkg_dolauncher jannovar-hgvs --jar jannovar-hgvs-0.16.jar
+ #java-pkg_dojar jannovar-htsjdk/target/jannovar-htsjdk-0.16.jar
+ #java-pkg_dolauncher jannovar-htsjdk --jar jannovar-htsjdk-0.16.jar
+ #java-pkg_dojar jannovar-core/target/jannovar-core-0.16.jar
+ #java-pkg_dolauncher jannovar-core --jar jannovar-core-0.16.jar
+ #java-pkg_dojar jannovar-filter/target/jannovar-filter-0.16.jar
+ #java-pkg_dolauncher jannovar-filter --jar jannovar-filter-0.16.jar
+ #java-pkg_dojar
jannovar-inheritance-checker/target/jannovar-inheritance-checker-0.16.jar
+ #java-pkg_dolauncher jannovar-inheritance-checker --jar
jannovar-inheritance-checker-0.16.jar
}
