commit: b7426d8f1df55eb09a50815dc95882363bb44895 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Mon Mar 25 11:56:28 2019 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Mon Mar 25 11:56:28 2019 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b7426d8f
sci-biology/tablet: still installs a mix of our and bundled jars We have only dev-java/htdjdk-2.3.0 in the tree as newer versions use gradle. The tablet-1.17.08.17 lacks the lib/htsjdk-2.0.11.jar so we cannot install it. Use sci-biology/tablet-bin instead. https://github.com/cropgeeks/tablet/issues/6 Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz> sci-biology/tablet/tablet-1.17.08.17.ebuild | 29 +++++++++++++++++++++-------- sci-biology/tablet/tablet-9999.ebuild | 17 ++++++++++++++--- 2 files changed, 35 insertions(+), 11 deletions(-) diff --git a/sci-biology/tablet/tablet-1.17.08.17.ebuild b/sci-biology/tablet/tablet-1.17.08.17.ebuild index 08a272961..158caba78 100644 --- a/sci-biology/tablet/tablet-1.17.08.17.ebuild +++ b/sci-biology/tablet/tablet-1.17.08.17.ebuild @@ -16,7 +16,7 @@ if [ "$PV" == "9999" ]; then KEYWORDS="" else SRC_URI="https://github.com/cropgeeks/tablet/archive/${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="" + KEYWORDS="" # lacks lib/htsjdk-2.0.11.jar fi LICENSE="BSD-2" @@ -29,11 +29,17 @@ DEPEND="${PYTHON_DEPS} >=virtual/jdk-1.8:*" RDEPEND="${PYTHON_DEPS} >=virtual/jre-1.8:* - >=dev-java/commons-compress-1.4.1" -# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, htsjdk-2.11.0.jar -# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not sci-biology/samtools either - -S="${WORKDIR}" + >=dev-java/commons-compress-1.4.1 + dev-java/htsjdk" +# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar +# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 +# samtools-linux64.jar is not sci-biology/samtools but 0.1.12a (r862) +# needs htsjdk-2.0.11.jar + +src_compile(){ + mkdir -p classes || die + ant jar || die +} src_install() { java-pkg_dojar lib/tablet.jar @@ -41,8 +47,15 @@ src_install() { 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/htsjdk*.jar # is htsjdk-2.11.0 in tablet-1.17.08.17 + java-pkg_dojar lib/samtools-all.jar + if [ "${ABI}" == "amd64" ]; then + java-pkg_dojar lib/samtools-linux64.jar + fi + if [ "${ABI}" == "x86" ]; then + java-pkg_dojar lib/samtools-linux32.jar + fi + # is the tar.gz tarball missing by mistake lib/htsjdk*.jar ? + # java-pkg_dojar lib/htsjdk*.jar # is htsjdk-2.11.0 in tablet-1.17.08.17 java-pkg_dojar lib/sqlite-jdbc*.jar echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet diff --git a/sci-biology/tablet/tablet-9999.ebuild b/sci-biology/tablet/tablet-9999.ebuild index 01759c6b4..5cebde785 100644 --- a/sci-biology/tablet/tablet-9999.ebuild +++ b/sci-biology/tablet/tablet-9999.ebuild @@ -31,9 +31,14 @@ RDEPEND="${PYTHON_DEPS} >=virtual/jre-1.8:* >=dev-java/commons-compress-1.4.1" # contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, htsjdk-2.11.0.jar -# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not sci-biology/samtools +# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 +# samtools-linux64.jar is not sci-biology/samtools but 0.1.12a (r862) #S="${WORKDIR}" +src_compile(){ + mkdir -p classes || die + ant jar || die +} src_install() { java-pkg_dojar lib/tablet.jar @@ -41,8 +46,14 @@ src_install() { java-pkg_dojar lib/tablet-resources.jar java-pkg_dojar lib/flamingo.jar java-pkg_dojar lib/scri-commons.jar - java-pkg_dojar lib/samtools*.jar - java-pkg_dojar lib/htsjdk*.jar + java-pkg_dojar lib/samtools-all.jar + if [ "${ABI}" == "amd64" ]; then + java-pkg_dojar lib/samtools-linux64.jar + fi + if [ "${ABI}" == "x86" ]; then + java-pkg_dojar lib/samtools-linux32.jar + fi + java-pkg_dojar lib/htsjdk*.jar # is htsjdk-2.11.0 in tablet-1.17.08.17 java-pkg_dojar lib/sqlite-jdbc*.jar echo "PATH=${EPREFIX}/usr/share/${PN}" > 99Tablet
