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

[Martin Mokrejs]

commit:     2757bce9c317df0e626a3487e41be845ea4c37d6
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Feb 20 10:32:07 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Feb 20 10:32:07 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2757bce9

sci-biology/tablet-bin: use two alternative sed calls to distinguish normal and 
EPREFIX installations

Somehow the EPREFIX-enabled sed call breaks normal non-EPREFIX host 
installations.
Document bundled jar files.

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild 
b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
index 5819aeed8..4231c9411 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
@@ -39,6 +39,7 @@ DEPEND="${PYTHON_DEPS}
        >=virtual/jdk-1.8"
 RDEPEND="${DEPEND}
                >=virtual/jre-1.8"
+# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
 
 S="${WORKDIR}"
 
@@ -73,8 +74,13 @@ src_install() {
        # make sure we force java to point a to $HOME which is inside our sanbox
        # directory area. We force -Duser.home . It seems also 
-Dinstall4j.userHome
        # could be done based on the figure shown at 
http://resources.ej-technologies.com/install4j/help/doc/
-       sed \
-               -e 's#"$app_java_home/bin/java" -Dinstall4j.jvmDir# 
'"${EPREFIX}""/usr/bin/java -Duser.home=${TMPDIR} -Dinstall4j.jvmDir 
-Djava.util.prefs.systemRoot=${TMPDIR}#" -i "${WORKDIR}"/${P}.sh || die
+       if [ -z "${EPREFIX}" ]; then
+               sed \
+               -e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" 
-Duser.home=${TMPDIR} -Dinstall4j.jvmDir 
-Djava.util.prefs.systemRoot=${TMPDIR}#" -i "${WORKDIR}"/${P}.sh || die
+       else
+               sed \
+                       -e 's#"$app_java_home/bin/java" -Dinstall4j.jvmDir# 
'"${EPREFIX}""/usr/bin/java -Duser.home=${TMPDIR} -Dinstall4j.jvmDir 
-Djava.util.prefs.systemRoot=${TMPDIR}#" -i "${WORKDIR}"/${P}.sh || die
+       fi
        sh \
                "${WORKDIR}"/${P}.sh \
                -q -overwrite \
@@ -82,7 +88,7 @@ src_install() {
                --destination="${ED}"/opt/Tablet \
                -dir "${ED}"/opt/Tablet || die
 
-       rm -rf "${ED}"/opt/Tablet/jre || die
+       rm -rf "${ED}"/opt/Tablet/jre "${ED}"/opt/Tablet/.install4j || die
 
        # this dies with tablet-bin-1.14.04.10 with
        #  * python2_7: running python_doscript 
/mnt/1TB/var/tmp/portage/sci-biology/tablet-bin-1.14.04.10/work/coveragestats.py
@@ -96,6 +102,7 @@ src_install() {
        insinto /opt/Tablet/utils
        doins coveragestats.py
 
-       echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
-       doenvd 99Tablet
+       # do not use 99Tablet to avoid file collision with sci-biology/tablet
+       echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet-bin
+       doenvd 99Tablet-bin
 }