[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/files/, sci-biology/tablet-bin/
commit: ecd3b3602cb2f9728ea08d2cd72c3d37f8373f93
Author: Andrew Ammerlaan riseup net>
AuthorDate: Mon Feb 1 05:07:34 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Mon Feb 1 05:07:34 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ecd3b360
sci-biology/tablet-bin: drop pack, py2 only
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/tablet-bin/files/response.varfile | 11 ---
sci-biology/tablet-bin/metadata.xml| 12 ---
.../tablet-bin/tablet-bin-1.20.12.24.ebuild| 105 -
3 files changed, 128 deletions(-)
diff --git a/sci-biology/tablet-bin/files/response.varfile
b/sci-biology/tablet-bin/files/response.varfile
deleted file mode 100644
index cfa2e6808..0
--- a/sci-biology/tablet-bin/files/response.varfile
+++ /dev/null
@@ -1,11 +0,0 @@
-#install4j response file for Tablet x.xx.xx.xx
-#Mon Jan 24 11:35:29 GMT 2011
-executeLauncherAction$Boolean=false
-sys.programGroupDisabled$Boolean=true
-# somehow, this happens: ln -s
/scratch/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/tablet
/usr/local/bin/tablet
-# # that happens because
/scratch/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/response.varfile
does not reflect our values
-sys.symlinkDir="${D}"usr/bin
-#sys.symlinkDir=/scratch/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/usr/bin
-sys.languageId=en
-sys.userHome="${D}"/../temp
-sys.installationDir="${D}"opt/Tablet
diff --git a/sci-biology/tablet-bin/metadata.xml
b/sci-biology/tablet-bin/metadata.xml
deleted file mode 100644
index 138cb7705..0
--- a/sci-biology/tablet-bin/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd";>
-
-
- mmokr...@fold.natur.cuni.cz
- Martin Mokrejs
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
diff --git a/sci-biology/tablet-bin/tablet-bin-1.20.12.24.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.20.12.24.ebuild
deleted file mode 100644
index 697ae0d36..0
--- a/sci-biology/tablet-bin/tablet-bin-1.20.12.24.ebuild
+++ /dev/null
@@ -1,105 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit java-pkg-2 python-r1
-
-DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
-HOMEPAGE="https://ics.hutton.ac.uk/tablet";
-SRC_URI="
- x86? (
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x86_$(ver_rs
0-3 _).sh -> ${P}.sh )
- amd64? (
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x64_$(ver_rs
0-3 _).sh -> ${P}.sh )
- https://bioinf.hutton.ac.uk/tablet/additional/coveragestats.py";
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
- app-text/dos2unix
- >=virtual/jdk-1.8:*"
-RDEPEND="${DEPEND}
- >=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_unpack() {
- local file
- for file in ${A}; do
- cp "${DISTDIR}"/${file} "${WORKDIR}" || die
- done
-}
-
-src_install() {
- # In theory it seems this binary package could be installed through ant
- # instead of the install4j package which is not easy to be forced
- # non-interactive. The below approach via install4j is not ideal but
works.
- sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile >
"${WORKDIR}"/response.varfile || die "sed failed"
-
- # the intallation script somehow does not pickup
- # -varfile="${DISTDIR}"/response.varfile from the commandline and
therefore
- # we place the file rather directly into the place where it should
reside.
- # In the file you can read details how the variables were mangled. For
- # example, the trick with sys.symlinkDir in the response.varfile is to
- # disable the installation process to symlink from /usr/local/bin/table
to
- # /opt/Tablet/tablet. That was logged in that file with the following
line:
- #
- #
/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log:
- # Variable changed: sys.symlinkDir=/usr/local/bin[class
java.lang.String]
- #
- # The file is then left on the installed system in
"${D}"/opt/Tablet/.install4j/response.varfile
- dodir /opt/Tablet/.install4j
- cat "${WORKDIR}"/response.varfile >
"${ED}"/opt/Tablet/.install4j/response.varfile || die
-
- # make sure we force java to point a to $HOME which is inside our s
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
commit: 6ff0fe6421ccb04c1746e46ea2b61fc02d4c0f98
Author: Andrew Ammerlaan riseup net>
AuthorDate: Mon Jan 18 13:48:11 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Mon Jan 18 13:48:11 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6ff0fe64
sci-biology/tablet-bin: fix fetching
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
...bin-1.17.08.17.ebuild => tablet-bin-1.20.12.24.ebuild} | 15 +++
1 file changed, 7 insertions(+), 8 deletions(-)
diff --git a/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.20.12.24.ebuild
similarity index 89%
rename from sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
rename to sci-biology/tablet-bin/tablet-bin-1.20.12.24.ebuild
index fb89b4208..697ae0d36 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.20.12.24.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
PYTHON_COMPAT=( python2_7 )
@@ -10,14 +10,13 @@ inherit java-pkg-2 python-r1
DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
HOMEPAGE="https://ics.hutton.ac.uk/tablet";
SRC_URI="
- x86? (
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x86_$(replace_all_version_separators
_).sh -> ${P}.sh )
- amd64? (
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x64_$(replace_all_version_separators
_).sh -> ${P}.sh )
- http://bioinf.hutton.ac.uk/tablet/additional/coveragestats.py";
+ x86? (
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x86_$(ver_rs
0-3 _).sh -> ${P}.sh )
+ amd64? (
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x64_$(ver_rs
0-3 _).sh -> ${P}.sh )
+ https://bioinf.hutton.ac.uk/tablet/additional/coveragestats.py";
LICENSE="BSD-2"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
+KEYWORDS=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
@@ -68,7 +67,7 @@ src_install() {
-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
+ -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 \
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
commit: 6520aa795d79c63f0566d8b1059acb95899f8f81
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Mar 25 09:40:18 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Mar 25 09:40:18 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6520aa79
sci-biology/tablet-bin: update license
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild | 14 +-
1 file changed, 1 insertion(+), 13 deletions(-)
diff --git a/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
index 51f2d7921..fb89b4208 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
@@ -14,19 +14,7 @@ SRC_URI="
amd64? (
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x64_$(replace_all_version_separators
_).sh -> ${P}.sh )
http://bioinf.hutton.ac.uk/tablet/additional/coveragestats.py";
-# Upstream says regarding source code unavailability:
-# Tablet uses a modified version of the BSD License which has been edited to
-# remove references to distribution and use in source forms. This means that
-# we are happy for you to distribute and use Tablet however you please, but we
-# do not (yet) want to make the source code publicly available.
-
-# The licence file itself is in the installer, and ends up on disk after
-# installation at /opt/Tablet/docs/tablet.html
-# The original BSD licence was modified to remove references to distribution
-# and use in source forms, because we cannot make the source code available
-# for Tablet.
-
-LICENSE="Tablet"
+LICENSE="BSD-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
commit: ad4cf1cc47d4dadaec146d2515ae9645c062adcd
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Mar 25 09:30:59 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Mar 25 09:30:59 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ad4cf1cc
sci-biology/tablet-bin: use https for the new homepage
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
index 6934743b1..51f2d7921 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
inherit java-pkg-2 python-r1
DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
-HOMEPAGE="http://ics.hutton.ac.uk/tablet/";
+HOMEPAGE="https://ics.hutton.ac.uk/tablet";
SRC_URI="
x86? (
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x86_$(replace_all_version_separators
_).sh -> ${P}.sh )
amd64? (
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x64_$(replace_all_version_separators
_).sh -> ${P}.sh )
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
commit: 9f62533afcb9014961a43534237d3a31a7aa4d00
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Mar 25 09:03:15 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Mar 25 09:03:15 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9f62533a
sci-biology/tablet-bin: version bump, ebuild cleanup
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
...tablet-bin-1.16.09.06.ebuild => tablet-bin-1.17.08.17.ebuild} | 9 +
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
similarity index 93%
rename from sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
rename to sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
index 401515e00..6934743b1 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -10,8 +10,8 @@ inherit java-pkg-2 python-r1
DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
HOMEPAGE="http://ics.hutton.ac.uk/tablet/";
SRC_URI="
- x86? (
http://bioinf.hutton.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators
_).sh -> ${P}.sh )
- amd64? (
http://bioinf.hutton.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators
_).sh -> ${P}.sh )
+ x86? (
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x86_$(replace_all_version_separators
_).sh -> ${P}.sh )
+ amd64? (
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x64_$(replace_all_version_separators
_).sh -> ${P}.sh )
http://bioinf.hutton.ac.uk/tablet/additional/coveragestats.py";
# Upstream says regarding source code unavailability:
@@ -36,7 +36,8 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
app-text/dos2unix
>=virtual/jdk-1.8:*"
-RDEPEND="${DEPEND}"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.8:*"
# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not
sci-biology/samtools either
# replacing picard.jar with a symlink to picard.jar from sci-biology.picard
does not help either
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
commit: 943bda111f0078c3aff0f3b6419fcd4c6a8a7fa9
Author: Justin Lecher gentoo org>
AuthorDate: Mon Apr 2 12:40:39 2018 +
Commit: Justin Lecher gentoo org>
CommitDate: Mon Apr 2 12:40:39 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=943bda11
sci-biology/tablet-bin: FIX specify an explicit slot
Signed-off-by: Justin Lecher gentoo.org>
Package-Manager: Portage-2.3.27, Repoman-2.3.9
sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild | 9 -
1 file changed, 4 insertions(+), 5 deletions(-)
diff --git a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
index c81c64e9b..401515e00 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
PYTHON_COMPAT=( python2_7 )
@@ -35,9 +35,8 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
app-text/dos2unix
- >=virtual/jdk-1.8"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.8"
+ >=virtual/jdk-1.8:*"
+RDEPEND="${DEPEND}"
# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not
sci-biology/samtools either
# replacing picard.jar with a symlink to picard.jar from sci-biology.picard
does not help either
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
commit: 8be5fc83dfffd37f2b607cfcbe6b17be01745594
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Mon Feb 20 11:59:55 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Feb 20 11:59:55 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=8be5fc83
sci-biology/tablet-bin: do not zap bundled jar files as we do not have a
package for them in Gentoo
Maybe except picard.jar while upstream uses picard-1.113 in tablet-1.16.09.06.
We should be around 2.0.3 with sci-biology/picard- as of now.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild | 11 +++
1 file changed, 11 insertions(+)
diff --git a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
index 4231c9411..6fc765e54 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
@@ -40,6 +40,8 @@ DEPEND="${PYTHON_DEPS}
RDEPEND="${DEPEND}
>=virtual/jre-1.8"
# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
+# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not
sci-biology/samtools either
+# replacing picard.jar with a symlink to picard.jar from sci-biology.picard
does not help either
S="${WORKDIR}"
@@ -90,6 +92,15 @@ src_install() {
rm -rf "${ED}"/opt/Tablet/jre "${ED}"/opt/Tablet/.install4j || die
+ # zap bundled jars
+ # do not zap even picard.jar because tablet does not start then with an
error:
+ # java.lang.NoClassDefFoundError: net/sf/samtools/SAMReadGroupRecord
+ # not even a symlink to "${EPREFIX}"/usr/share/picard/lib/picard.jar
helps
+ #
+ # for f in picard.jar; do
+ # rm -f "${ED}"/opt/Tablet/lib/"$f" || die
+ # done
+
# this dies with tablet-bin-1.14.04.10 with
# * python2_7: running python_doscript
/mnt/1TB/var/tmp/portage/sci-biology/tablet-bin-1.14.04.10/work/coveragestats.py
# * The file has incompatible shebang:
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
commit: 2757bce9c317df0e626a3487e41be845ea4c37d6
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Mon Feb 20 10:32:07 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Feb 20 10:32:07 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2757bce9
sci-biology/tablet-bin: use two alternative sed calls to distinguish normal and
EPREFIX installations
Somehow the EPREFIX-enabled sed call breaks normal non-EPREFIX host
installations.
Document bundled jar files.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild | 17 -
1 file changed, 12 insertions(+), 5 deletions(-)
diff --git a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
index 5819aeed8..4231c9411 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
@@ -39,6 +39,7 @@ DEPEND="${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=${EPREFIX}/opt/Tablet" > 99Tablet-bin
+ doenvd 99Tablet-bin
}
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
commit: 0d0b63f4cc9c906555373259334a830126d98e45
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sun Feb 19 10:09:07 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Feb 19 10:09:07 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0d0b63f4
sci-biology/tablet-bin: fix sed hackery for EPREFIX installations
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
index 78b7b5386..5819aeed8 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
@@ -74,7 +74,7 @@ src_install() {
# directory area. We force -Duser.home . It seems also
-Dinstall4j.userHome
# could be done based on the figure shown at
http://resources.ej-technologies.com/install4j/help/doc/
sed \
- -e "s#/bin/java\" -Dinstall4j.jvmDir#"${EPREFIX}"/bin/java\"
-Duser.home=${TMPDIR} -Dinstall4j.jvmDir
-Djava.util.prefs.systemRoot=${TMPDIR}#" -i "${WORKDIR}"/${P}.sh || die
+ -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
sh \
"${WORKDIR}"/${P}.sh \
-q -overwrite \
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
commit: 2547daf2073118349d378e765f96d227104a7aa1
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sun Feb 19 00:51:34 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Feb 19 00:51:34 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2547daf2
sci-biology/tablet-bin: version bump
Pass '-Djava.util.prefs.systemRoot=${TMPDIR}' to java to avoid permission denied
when writing to /etc/.java/.systemPrefs (outside our sandbox)
The /opt/Tablet/tablet wrapper falsely issues error although am on Oracle JDK
1.8.0.121 [oracle-jdk-bin-1.8]:
java.lang.UnsupportedClassVersionError: tablet/gui/Tablet : Unsupported
major.minor version 52.0
However, 'java -jar /opt/Tablet/lib/tablet.jar' runs fine.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
...blet-bin-1.15.09.01.ebuild => tablet-bin-1.16.09.06.ebuild} | 10 +-
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/sci-biology/tablet-bin/tablet-bin-1.15.09.01.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
similarity index 93%
rename from sci-biology/tablet-bin/tablet-bin-1.15.09.01.ebuild
rename to sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
index d894aa183..78b7b5386 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.15.09.01.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -35,9 +35,10 @@ IUSE=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
- app-text/dos2unix"
+ app-text/dos2unix
+ >=virtual/jdk-1.8"
RDEPEND="${DEPEND}
- virtual/jre"
+ >=virtual/jre-1.8"
S="${WORKDIR}"
@@ -73,8 +74,7 @@ src_install() {
# 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#/bin/java\" -Dinstall4j.jvmDir#/bin/java\"
-Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \
- -i "${WORKDIR}"/${P}.sh || die
+ -e "s#/bin/java\" -Dinstall4j.jvmDir#"${EPREFIX}"/bin/java\"
-Duser.home=${TMPDIR} -Dinstall4j.jvmDir
-Djava.util.prefs.systemRoot=${TMPDIR}#" -i "${WORKDIR}"/${P}.sh || die
sh \
"${WORKDIR}"/${P}.sh \
-q -overwrite \
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
commit: 03e6391c2d30887d78676f50bf050a121a5b6da4
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Apr 20 19:05:03 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Apr 20 19:05:03 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=03e6391c
sci-biology/tablet-bin: version bump; added coveragestats.py (requires dos2unix)
Package-Manager: portage-2.2.28
.../{tablet-bin-1.14.10.21.ebuild => tablet-bin-1.15.09.01.ebuild} | 6 +-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.15.09.01.ebuild
similarity index 96%
rename from sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild
rename to sci-biology/tablet-bin/tablet-bin-1.15.09.01.ebuild
index 6c0e63a..d894aa1 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.15.09.01.ebuild
@@ -34,7 +34,8 @@ IUSE=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-DEPEND="${PYTHON_DEPS}"
+DEPEND="${PYTHON_DEPS}
+ app-text/dos2unix"
RDEPEND="${DEPEND}
virtual/jre"
@@ -91,6 +92,9 @@ src_install() {
# * requested impl: python2.7
#
# python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
+ dos2unix "${WORKDIR}"/coveragestats.py coveragestats.py || die
+ insinto /opt/Tablet/utils
+ doins coveragestats.py
echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
doenvd 99Tablet
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
commit: 2e448f8cd4ae8fca64381058d48ea8e683234c0d
Author: Ted Tanberry gmail com>
AuthorDate: Sat Mar 28 12:08:22 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Sat Mar 28 12:08:22 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2e448f8c
sci-biology/tablet-bin: Update HOMEPAGE
sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild
index 4f36d7e..4026035 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild
@@ -9,7 +9,7 @@ PYTHON_COMPAT=( python{2_6,2_7} )
inherit java-pkg-2 python-r1
DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/";
+HOMEPAGE="http://ics.hutton.ac.uk/tablet/";
SRC_URI="
x86? (
http://bioinf.hutton.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators
_).sh -> ${P}.sh )
amd64? (
http://bioinf.hutton.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators
_).sh -> ${P}.sh )
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
commit: 0a5a7511e618764600d35bd6d03c08b1ecf7f0f9
Author: Ted Tanberry gmail com>
AuthorDate: Sun Mar 15 18:17:50 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Sun Mar 15 18:17:50 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0a5a7511
Updated sci-biology/tablet-bin to latest version, removed stale ebuilds.
sci-biology/tablet-bin/ChangeLog | 9 ++-
.../tablet-bin/tablet-bin-1.13.12.17.ebuild| 90 --
...4.04.10.ebuild => tablet-bin-1.14.10.21.ebuild} | 8 +-
3 files changed, 12 insertions(+), 95 deletions(-)
diff --git a/sci-biology/tablet-bin/ChangeLog b/sci-biology/tablet-bin/ChangeLog
index 7128ae0..6864475 100644
--- a/sci-biology/tablet-bin/ChangeLog
+++ b/sci-biology/tablet-bin/ChangeLog
@@ -1,7 +1,14 @@
# ChangeLog for sci-biology/tablet-bin
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*tablet-bin-1.14.10.21 (15 Mar 2015)
+
+ 15 Mar 2015; Ted Tanberry
+ +tablet-bin-1.14.10.21.ebuild,
+ -tablet-bin-1.13.12.17.ebuild, -tablet-bin-1.14.04.10.ebuild:
+ Version bump, update SRC_URI, remove dead ebuilds
+
16 Sep 2014; Christoph Junghans
tablet-bin-1.14.04.10.ebuild:
clean up
diff --git a/sci-biology/tablet-bin/tablet-bin-1.13.12.17.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.13.12.17.ebuild
deleted file mode 100644
index 7b7d001..000
--- a/sci-biology/tablet-bin/tablet-bin-1.13.12.17.ebuild
+++ /dev/null
@@ -1,90 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_6,2_7} )
-
-inherit java-pkg-2 python-r1
-
-DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/";
-SRC_URI="
- x86? (
http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators
_).sh -> ${P}.sh )
- amd64? (
http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators
_).sh -> ${P}.sh )
- http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py";
-
-# Upstream says regarding source code unavailability:
-# Tablet uses a modified version of the BSD License which has been edited to
-# remove references to distribution and use in source forms. This means that
-# we are happy for you to distribute and use Tablet however you please, but we
-# do not (yet) want to make the source code publicly available.
-
-# The licence file itself is in the installer, and ends up on disk after
-# installation at /opt/Tablet/docs/tablet.html
-# The original BSD licence was modified to remove references to distribution
-# and use in source forms, because we cannot make the source code available
-# for Tablet.
-
-LICENSE="Tablet"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}"
-RDEPEND="${DEPEND}
- virtual/jre"
-
-S="${WORKDIR}"
-
-src_unpack() {
- local file
- for file in ${A}; do
- cp "${DISTDIR}"/${file} "${WORKDIR}" || die
- done
-}
-
-src_install() {
- # In theory it seems this binary package could be installed through ant
- # instead of the install4j package which is not easy to be forced
- # non-interactive. The below approach via install4j is not ideal but
works.
- sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile >
"${WORKDIR}"/response.varfile || die "sed failed"
-
- # the intallation script somehow does not pickup
- # -varfile="${DISTDIR}"/response.varfile from the commandline and
therefore
- # we place the file rather directly into the place where it should
reside.
- # In the file you can read details how the variables were mangled. For
- # example, the trick with sys.symlinkDir in the response.varfile is to
- # disable the installation process to symlink from /usr/local/bin/table
to
- # /opt/Tablet/tablet. That was logged in that file with the following
line:
- #
- #
/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log:
- # Variable changed: sys.symlinkDir=/usr/local/bin[class
java.lang.String]
- #
- # The file is then left on the installed system in
"${D}"/opt/Tablet/.install4j/response.varfile
- dodir /opt/Tablet/.install4j
- cat "${WORKDIR}"/response.varfile >
"${ED}"/opt/Tablet/.install4j/response.varfile || die
-
- # 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#/bin/java\" -Dinstall4j.jvmDir#/bin/java\"
-Du
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
commit: a9ed26d1da41bed56c21a42495c7be6f80da93d7
Author: Christoph Junghans gentoo org>
AuthorDate: Tue Sep 16 16:27:16 2014 +
Commit: Christoph Junghans gentoo org>
CommitDate: Tue Sep 16 16:27:16 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a9ed26d1
clean up
Package-Manager: portage-2.2.8-r1
---
sci-biology/tablet-bin/ChangeLog| 4
sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild | 2 +-
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-biology/tablet-bin/ChangeLog b/sci-biology/tablet-bin/ChangeLog
index 8b38781..7128ae0 100644
--- a/sci-biology/tablet-bin/ChangeLog
+++ b/sci-biology/tablet-bin/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 16 Sep 2014; Christoph Junghans
+ tablet-bin-1.14.04.10.ebuild:
+ clean up
+
*tablet-bin-1.14.04.10 (02 Jul 2014)
02 Jul 2014; Martin Mokrejs
diff --git a/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild
index 1a0fdf1..d13ad0c 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild
@@ -83,7 +83,7 @@ src_install() {
rm -rf "${ED}"/opt/Tablet/jre || die
-# this dies with tablet-bin-1.14.04.10 with
+ # 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
# * The file has incompatible shebang:
# * file: /usr/lib/python-exec/python2.7/coveragestats.py
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
commit: 01ff3a2d6b36716aa83e749acfeb4cc09e076ba8
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Jul 2 22:40:49 2014 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Jul 2 22:40:49 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=01ff3a2d
sci-biology/tablet-bin: version bump; updated the license
Package-Manager: portage-2.2.7
---
sci-biology/tablet-bin/ChangeLog | 6 ++
.../tablet-bin/tablet-bin-1.14.04.10.ebuild| 97 ++
2 files changed, 103 insertions(+)
diff --git a/sci-biology/tablet-bin/ChangeLog b/sci-biology/tablet-bin/ChangeLog
index d48473a..8b38781 100644
--- a/sci-biology/tablet-bin/ChangeLog
+++ b/sci-biology/tablet-bin/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*tablet-bin-1.14.04.10 (02 Jul 2014)
+
+ 02 Jul 2014; Martin Mokrejs
+ +tablet-bin-1.14.04.10.ebuild:
+ sci-biology/tablet-bin: version bump; updated the license
+
*tablet-bin-1.13.12.17 (20 Jan 2014)
20 Jan 2014; Martin Mokrejs
diff --git a/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild
new file mode 100644
index 000..1a0fdf1
--- /dev/null
+++ b/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild
@@ -0,0 +1,97 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit java-pkg-2 python-r1
+
+DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
+HOMEPAGE="http://bioinf.scri.ac.uk/tablet/";
+SRC_URI="
+ x86? (
http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators
_).sh -> ${P}.sh )
+ amd64? (
http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators
_).sh -> ${P}.sh )
+ http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py";
+
+# Upstream says regarding source code unavailability:
+# Tablet uses a modified version of the BSD License which has been edited to
+# remove references to distribution and use in source forms. This means that
+# we are happy for you to distribute and use Tablet however you please, but we
+# do not (yet) want to make the source code publicly available.
+
+# The licence file itself is in the installer, and ends up on disk after
+# installation at /opt/Tablet/docs/tablet.html
+# The original BSD licence was modified to remove references to distribution
+# and use in source forms, because we cannot make the source code available
+# for Tablet.
+
+LICENSE="Tablet"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}"
+RDEPEND="${DEPEND}
+ virtual/jre"
+
+S="${WORKDIR}"
+
+src_unpack() {
+ local file
+ for file in ${A}; do
+ cp "${DISTDIR}"/${file} "${WORKDIR}" || die
+ done
+}
+
+src_install() {
+ # In theory it seems this binary package could be installed through ant
+ # instead of the install4j package which is not easy to be forced
+ # non-interactive. The below approach via install4j is not ideal but
works.
+ sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile >
"${WORKDIR}"/response.varfile || die "sed failed"
+
+ # the intallation script somehow does not pickup
+ # -varfile="${DISTDIR}"/response.varfile from the commandline and
therefore
+ # we place the file rather directly into the place where it should
reside.
+ # In the file you can read details how the variables were mangled. For
+ # example, the trick with sys.symlinkDir in the response.varfile is to
+ # disable the installation process to symlink from /usr/local/bin/table
to
+ # /opt/Tablet/tablet. That was logged in that file with the following
line:
+ #
+ #
/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log:
+ # Variable changed: sys.symlinkDir=/usr/local/bin[class
java.lang.String]
+ #
+ # The file is then left on the installed system in
"${D}"/opt/Tablet/.install4j/response.varfile
+ dodir /opt/Tablet/.install4j
+ cat "${WORKDIR}"/response.varfile >
"${ED}"/opt/Tablet/.install4j/response.varfile || die
+
+ # make sure we force java to point a to $HOME which is inside our sanbox
+ # directory area. We force -Duser.home . It seems also
-Dinstall4j.userHome
+ # could be done based on the figure shown at
http://resources.ej-technologies.com/install4j/help/doc/
+ sed \
+ -e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\"
-Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \
+ -i "${WORKDIR}"/${P}.sh || die
+ sh \
+ "${WORKDIR}"/${P}.sh \
+ -q -overwrite \
+ -var
