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| author |   Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2019-03-25 12:56:28 +0100 |
|---|---|---|
| committer | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2019-03-25 12:56:28 +0100 |
| commit | b7426d8f1df55eb09a50815dc95882363bb44895 (patch) | |
| tree | 0686f9cc7a68046934c54bb35c73dbd862bbcb30 /sci-biology/tablet | |
| parent | dev-java/htsjdk: drop old 2.1.0 version (diff) | |
| download | sci-b7426d8f1df55eb09a50815dc95882363bb44895.tar.gz sci-b7426d8f1df55eb09a50815dc95882363bb44895.tar.bz2 sci-b7426d8f1df55eb09a50815dc95882363bb44895.zip | |
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@fold.natur.cuni.cz>
Diffstat (limited to 'sci-biology/tablet')
| -rw-r--r-- | sci-biology/tablet/tablet-1.17.08.17.ebuild | 29 | ||||
| -rw-r--r-- | 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 |