* [gentoo-commits] proj/sci:master commit in: sci-biology/tablet/
@ 2014-07-02 22:42 Martin Mokrejs
0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2014-07-02 22:42 UTC (permalink / raw
To: gentoo-commits
commit: 520a2dd61f2a9b4716d34a975cd43dbefba6c41d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jul 2 22:39:35 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jul 2 22:39:35 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=520a2dd6
sci-biology/tablet: cleaned up the ebuilds, they compile and install but the bundled samtools-*.jar is not found; updated the license
Package-Manager: portage-2.2.7
---
sci-biology/tablet/ChangeLog | 8 +++
sci-biology/tablet/tablet-1.13.12.17.ebuild | 85 ++++++++---------------------
sci-biology/tablet/tablet-1.14.04.10.ebuild | 51 +++++++++++++++++
sci-biology/tablet/tablet-9999.ebuild | 77 +++++---------------------
4 files changed, 96 insertions(+), 125 deletions(-)
diff --git a/sci-biology/tablet/ChangeLog b/sci-biology/tablet/ChangeLog
index 0080ef2..0cca8d8 100644
--- a/sci-biology/tablet/ChangeLog
+++ b/sci-biology/tablet/ChangeLog
@@ -2,6 +2,14 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*tablet-1.14.04.10 (02 Jul 2014)
+
+ 02 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +tablet-1.14.04.10.ebuild, -Manifest, tablet-1.13.12.17.ebuild,
+ tablet-9999.ebuild:
+ sci-biology/tablet: cleaned up the ebuilds, they compile and install but the
+ bundled samtools-*.jar is not found
+
*tablet-1.13.12.17 (28 Mar 2014)
*tablet-9999 (28 Mar 2014)
diff --git a/sci-biology/tablet/tablet-1.13.12.17.ebuild b/sci-biology/tablet/tablet-1.13.12.17.ebuild
index 112709b..1940cb9 100644
--- a/sci-biology/tablet/tablet-1.13.12.17.ebuild
+++ b/sci-biology/tablet/tablet-1.13.12.17.ebuild
@@ -6,84 +6,45 @@ EAPI=5
PYTHON_COMPAT=( python{2_6,2_7} )
-inherit java-pkg-2 python-r1
+inherit java-pkg-2 java-ant-2 python-r1
+
+# [ "$PV" == "9999" ] && inherit subversion
+inherit subversion
DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
-SRC_URI="
- x86? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh )
- amd64? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators _).sh -> ${P}.sh )
- http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
-
-# Upstream says regarding source code unavailability:
-# Tablet uses a modified version of the BSD License which has been edited to
-# remove references to distribution and use in source forms. This means that
-# we are happy for you to distribute and use Tablet however you please, but we
-# do not (yet) want to make the source code publicly available.
-
-# The licence file itself is in the installer, and ends up on disk after
-# installation at /opt/Tablet/docs/tablet.html
-# The original BSD licence was modified to remove references to distribution
-# and use in source forms, because we cannot make the source code available
-# for Tablet.
+if [ "$PV" == "9999" ]; then
+ ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/"
+ KEYWORDS=""
+else
+ ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
+ KEYWORDS=""
+fi
LICENSE="Tablet"
SLOT="0"
-KEYWORDS=""
IUSE=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-DEPEND="${PYTHON_DEPS}"
+DEPEND="${PYTHON_DEPS}
+ >=virtual/jdk-1.7"
RDEPEND="${DEPEND}
- virtual/jre"
+ >=virtual/jre-1.7
+ sci-biology/samtools
+ sci-biology/picard
+ dev-db/sqlite"
S="${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 \
- -varfile="${DISTDIR}"/response.varfile \
- --destination="${ED}"/opt/Tablet \
- -dir "${ED}"/opt/Tablet || die
-
- rm -rf "${ED}"/opt/Tablet/jre || die
+ java-pkg_dojar lib/tablet-resources.jar || die
+ java-pkg_dojar lib/tablet.jar || die
+ java-pkg_dojar lib/flamingo.jar || die
+ java-pkg_dojar lib/scri-commons.jar || die
+ java-pkg_dojar lib/samtools*.jar || die
- python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
+ dobin www/additional/coveragestats.py
echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
doenvd 99Tablet || die
diff --git a/sci-biology/tablet/tablet-1.14.04.10.ebuild b/sci-biology/tablet/tablet-1.14.04.10.ebuild
new file mode 100644
index 0000000..1940cb9
--- /dev/null
+++ b/sci-biology/tablet/tablet-1.14.04.10.ebuild
@@ -0,0 +1,51 @@
+# 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 java-ant-2 python-r1
+
+# [ "$PV" == "9999" ] && inherit subversion
+inherit subversion
+
+DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
+HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
+if [ "$PV" == "9999" ]; then
+ ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/"
+ KEYWORDS=""
+else
+ ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
+ KEYWORDS=""
+fi
+
+LICENSE="Tablet"
+SLOT="0"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}
+ >=virtual/jdk-1.7"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.7
+ sci-biology/samtools
+ sci-biology/picard
+ dev-db/sqlite"
+
+S="${WORKDIR}"
+
+src_install() {
+ java-pkg_dojar lib/tablet-resources.jar || die
+ java-pkg_dojar lib/tablet.jar || die
+ java-pkg_dojar lib/flamingo.jar || die
+ java-pkg_dojar lib/scri-commons.jar || die
+ java-pkg_dojar lib/samtools*.jar || die
+
+ dobin www/additional/coveragestats.py
+
+ echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
+ doenvd 99Tablet || die
+}
diff --git a/sci-biology/tablet/tablet-9999.ebuild b/sci-biology/tablet/tablet-9999.ebuild
index 40472c7..1940cb9 100644
--- a/sci-biology/tablet/tablet-9999.ebuild
+++ b/sci-biology/tablet/tablet-9999.ebuild
@@ -6,9 +6,10 @@ EAPI=5
PYTHON_COMPAT=( python{2_6,2_7} )
-inherit java-pkg-2 java-ant-2 python-r1 eutils
+inherit java-pkg-2 java-ant-2 python-r1
-[ "$PV" == "9999" ] && inherit subversion
+# [ "$PV" == "9999" ] && inherit subversion
+inherit subversion
DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
@@ -20,23 +21,6 @@ else
KEYWORDS=""
fi
-#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 -> ${P}.sh )
-# http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
-
-# Upstream says regarding source code unavailability:
-# Tablet uses a modified version of the BSD License which has been edited to
-# remove references to distribution and use in source forms. This means that
-# we are happy for you to distribute and use Tablet however you please, but we
-# do not (yet) want to make the source code publicly available.
-
-# The licence file itself is in the installer, and ends up on disk after
-# installation at /opt/Tablet/docs/tablet.html
-# The original BSD licence was modified to remove references to distribution
-# and use in source forms, because we cannot make the source code available
-# for Tablet.
-
LICENSE="Tablet"
SLOT="0"
IUSE=""
@@ -44,56 +28,23 @@ IUSE=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
- virtual/jdk"
+ >=virtual/jdk-1.7"
RDEPEND="${DEPEND}
- virtual/jre"
+ >=virtual/jre-1.7
+ sci-biology/samtools
+ sci-biology/picard
+ dev-db/sqlite"
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 \
- -varfile="${DISTDIR}"/response.varfile \
- --destination="${ED}"/opt/Tablet \
- -dir "${ED}"/opt/Tablet || die
-
- rm -rf "${ED}"/opt/Tablet/jre || die
+ java-pkg_dojar lib/tablet-resources.jar || die
+ java-pkg_dojar lib/tablet.jar || die
+ java-pkg_dojar lib/flamingo.jar || die
+ java-pkg_dojar lib/scri-commons.jar || die
+ java-pkg_dojar lib/samtools*.jar || die
- python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
+ dobin www/additional/coveragestats.py
echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
doenvd 99Tablet || die
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/tablet/
@ 2015-01-09 15:35 Martin Mokrejs
0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2015-01-09 15:35 UTC (permalink / raw
To: gentoo-commits
commit: 7e7f17d08f0687cfec7abacfd986c465ca16ee18
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 9 15:31:02 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 9 15:31:02 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7e7f17d0
sci-biology/tablet: note the compilation from source is not coded into ebuild yet
Package-Manager: portage-2.2.7
---
sci-biology/tablet/ChangeLog | 6 +++++-
sci-biology/tablet/tablet-9999.ebuild | 4 +++-
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/sci-biology/tablet/ChangeLog b/sci-biology/tablet/ChangeLog
index 0cca8d8..7bd423c 100644
--- a/sci-biology/tablet/ChangeLog
+++ b/sci-biology/tablet/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/tablet
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> tablet-9999.ebuild:
+ sci-biology/tablet: note the compilation from source is not coded into ebuild
+ yet
+
*tablet-1.14.04.10 (02 Jul 2014)
02 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/tablet/tablet-9999.ebuild b/sci-biology/tablet/tablet-9999.ebuild
index 1940cb9..7923105 100644
--- a/sci-biology/tablet/tablet-9999.ebuild
+++ b/sci-biology/tablet/tablet-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -37,6 +37,8 @@ RDEPEND="${DEPEND}
S="${WORKDIR}"
+# TODO: do actually compile tablet from sources
+
src_install() {
java-pkg_dojar lib/tablet-resources.jar || die
java-pkg_dojar lib/tablet.jar || die
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/tablet/
@ 2015-02-18 16:41 Justin Lecher
0 siblings, 0 replies; 11+ messages in thread
From: Justin Lecher @ 2015-02-18 16:41 UTC (permalink / raw
To: gentoo-commits
commit: d45ebd290331cc672bded1ce4d9876a6b0505323
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 13:55:27 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 13:55:27 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d45ebd29
Add symlink
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
---
sci-biology/tablet/tablet-1.14.04.10.ebuild | 52 +----------------------------
1 file changed, 1 insertion(+), 51 deletions(-)
diff --git a/sci-biology/tablet/tablet-1.14.04.10.ebuild b/sci-biology/tablet/tablet-1.14.04.10.ebuild
deleted file mode 100644
index 1940cb9..0000000
--- a/sci-biology/tablet/tablet-1.14.04.10.ebuild
+++ /dev/null
@@ -1,51 +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 java-ant-2 python-r1
-
-# [ "$PV" == "9999" ] && inherit subversion
-inherit subversion
-
-DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
-if [ "$PV" == "9999" ]; then
- ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/"
- KEYWORDS=""
-else
- ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
- KEYWORDS=""
-fi
-
-LICENSE="Tablet"
-SLOT="0"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
- >=virtual/jdk-1.7"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.7
- sci-biology/samtools
- sci-biology/picard
- dev-db/sqlite"
-
-S="${WORKDIR}"
-
-src_install() {
- java-pkg_dojar lib/tablet-resources.jar || die
- java-pkg_dojar lib/tablet.jar || die
- java-pkg_dojar lib/flamingo.jar || die
- java-pkg_dojar lib/scri-commons.jar || die
- java-pkg_dojar lib/samtools*.jar || die
-
- dobin www/additional/coveragestats.py
-
- echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
- doenvd 99Tablet || die
-}
diff --git a/sci-biology/tablet/tablet-1.14.04.10.ebuild b/sci-biology/tablet/tablet-1.14.04.10.ebuild
new file mode 120000
index 0000000..a170f54
--- /dev/null
+++ b/sci-biology/tablet/tablet-1.14.04.10.ebuild
@@ -0,0 +1 @@
+tablet-9999.ebuild
\ No newline at end of file
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/tablet/
@ 2015-02-18 16:41 Justin Lecher
0 siblings, 0 replies; 11+ messages in thread
From: Justin Lecher @ 2015-02-18 16:41 UTC (permalink / raw
To: gentoo-commits
commit: 9edf23ce547ba5dc58d1d5d87dfb5895bee40bef
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 13:44:44 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 13:44:44 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9edf23ce
sci-biology/tablet: fix SLOT operators and dependencies
Package-Manager: portage-2.2.17
---
sci-biology/tablet/ChangeLog | 4 +++
sci-biology/tablet/tablet-1.13.12.17.ebuild | 51 -----------------------------
sci-biology/tablet/tablet-9999.ebuild | 28 +++++++---------
3 files changed, 16 insertions(+), 67 deletions(-)
diff --git a/sci-biology/tablet/ChangeLog b/sci-biology/tablet/ChangeLog
index 7bd423c..c27c747 100644
--- a/sci-biology/tablet/ChangeLog
+++ b/sci-biology/tablet/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Feb 2015; Justin Lecher <jlec@gentoo.org> -tablet-1.13.12.17.ebuild,
+ tablet-9999.ebuild:
+ sci-biology/tablet: fix SLOT operators and dependencies
+
09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> tablet-9999.ebuild:
sci-biology/tablet: note the compilation from source is not coded into ebuild
yet
diff --git a/sci-biology/tablet/tablet-1.13.12.17.ebuild b/sci-biology/tablet/tablet-1.13.12.17.ebuild
deleted file mode 100644
index 1940cb9..0000000
--- a/sci-biology/tablet/tablet-1.13.12.17.ebuild
+++ /dev/null
@@ -1,51 +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 java-ant-2 python-r1
-
-# [ "$PV" == "9999" ] && inherit subversion
-inherit subversion
-
-DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
-if [ "$PV" == "9999" ]; then
- ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/"
- KEYWORDS=""
-else
- ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
- KEYWORDS=""
-fi
-
-LICENSE="Tablet"
-SLOT="0"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
- >=virtual/jdk-1.7"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.7
- sci-biology/samtools
- sci-biology/picard
- dev-db/sqlite"
-
-S="${WORKDIR}"
-
-src_install() {
- java-pkg_dojar lib/tablet-resources.jar || die
- java-pkg_dojar lib/tablet.jar || die
- java-pkg_dojar lib/flamingo.jar || die
- java-pkg_dojar lib/scri-commons.jar || die
- java-pkg_dojar lib/samtools*.jar || die
-
- dobin www/additional/coveragestats.py
-
- echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
- doenvd 99Tablet || die
-}
diff --git a/sci-biology/tablet/tablet-9999.ebuild b/sci-biology/tablet/tablet-9999.ebuild
index 7923105..5d8f545 100644
--- a/sci-biology/tablet/tablet-9999.ebuild
+++ b/sci-biology/tablet/tablet-9999.ebuild
@@ -4,14 +4,14 @@
EAPI=5
-PYTHON_COMPAT=( python{2_6,2_7} )
+PYTHON_COMPAT=( python2_7 )
inherit java-pkg-2 java-ant-2 python-r1
# [ "$PV" == "9999" ] && inherit subversion
inherit subversion
-DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
+DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
if [ "$PV" == "9999" ]; then
ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/"
@@ -28,26 +28,22 @@ IUSE=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
- >=virtual/jdk-1.7"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.7
+ >=virtual/jdk-1.7:*"
+RDEPEND="${PYTHON_DEPS}
+ >=virtual/jre-1.7:*
sci-biology/samtools
sci-biology/picard
- dev-db/sqlite"
+ dev-db/sqlite:3"
S="${WORKDIR}"
-# TODO: do actually compile tablet from sources
-
src_install() {
- java-pkg_dojar lib/tablet-resources.jar || die
- java-pkg_dojar lib/tablet.jar || die
- java-pkg_dojar lib/flamingo.jar || die
- java-pkg_dojar lib/scri-commons.jar || die
- java-pkg_dojar lib/samtools*.jar || die
-
- dobin www/additional/coveragestats.py
+ java-pkg_dojar lib/tablet-resources.jar
+ java-pkg_dojar lib/tablet.jar
+ java-pkg_dojar lib/flamingo.jar
+ java-pkg_dojar lib/scri-commons.jar
+ java-pkg_dojar lib/samtools*.jar
echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
- doenvd 99Tablet || die
+ doenvd 99Tablet
}
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/tablet/
@ 2017-02-19 0:54 Martin Mokrejs
0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2017-02-19 0:54 UTC (permalink / raw
To: gentoo-commits
commit: 7c9d1fc1ef91728d38504e7c07a363d4b397ca3d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Feb 19 00:54:34 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Feb 19 00:54:34 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7c9d1fc1
sci-biology/tablet: version bump
Fix required java version to 1.8
Seems 1.16.09.06 is under upstream's SVN commit #876.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
...-1.14.04.10.ebuild => tablet-1.15.09.01.ebuild} | 24 ++++++++++++----------
...-1.14.04.10.ebuild => tablet-1.16.09.06.ebuild} | 6 +++---
sci-biology/tablet/tablet-9999.ebuild | 8 ++++----
3 files changed, 20 insertions(+), 18 deletions(-)
diff --git a/sci-biology/tablet/tablet-1.14.04.10.ebuild b/sci-biology/tablet/tablet-1.15.09.01.ebuild
similarity index 67%
copy from sci-biology/tablet/tablet-1.14.04.10.ebuild
copy to sci-biology/tablet/tablet-1.15.09.01.ebuild
index d8aa02c19..2d30b71bb 100644
--- a/sci-biology/tablet/tablet-1.14.04.10.ebuild
+++ b/sci-biology/tablet/tablet-1.15.09.01.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
# $Id$
@@ -18,7 +18,7 @@ if [ "$PV" == "9999" ]; then
KEYWORDS=""
else
ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
- KEYWORDS=""
+ KEYWORDS="~amd64 ~x86"
fi
LICENSE="Tablet"
@@ -28,9 +28,9 @@ IUSE=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
- >=virtual/jdk-1.7:*"
+ >=virtual/jdk-1.8:*"
RDEPEND="${PYTHON_DEPS}
- >=virtual/jre-1.7:*
+ >=virtual/jre-1.8:*
sci-biology/samtools
sci-biology/picard
dev-db/sqlite:3"
@@ -38,12 +38,14 @@ RDEPEND="${PYTHON_DEPS}
S="${WORKDIR}"
src_install() {
- java-pkg_dojar lib/tablet-resources.jar
- java-pkg_dojar lib/tablet.jar
- java-pkg_dojar lib/flamingo.jar
- java-pkg_dojar lib/scri-commons.jar
- java-pkg_dojar lib/samtools*.jar
-
- echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
+ cd lib || die
+ java-pkg_dojar tablet.jar
+ java-pkg_dolauncher ${PN}
+ java-pkg_dojar tablet-resources.jar
+ java-pkg_dojar flamingo.jar
+ java-pkg_dojar scri-commons.jar
+ java-pkg_dojar samtools*.jar
+
+ echo "PATH=${EPREFIX}/usr/share/${PN}/" > 99Tablet
doenvd 99Tablet
}
diff --git a/sci-biology/tablet/tablet-1.14.04.10.ebuild b/sci-biology/tablet/tablet-1.16.09.06.ebuild
similarity index 92%
rename from sci-biology/tablet/tablet-1.14.04.10.ebuild
rename to sci-biology/tablet/tablet-1.16.09.06.ebuild
index d8aa02c19..c4be1406f 100644
--- a/sci-biology/tablet/tablet-1.14.04.10.ebuild
+++ b/sci-biology/tablet/tablet-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
# $Id$
@@ -28,9 +28,9 @@ IUSE=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
- >=virtual/jdk-1.7:*"
+ >=virtual/jdk-1.8:*"
RDEPEND="${PYTHON_DEPS}
- >=virtual/jre-1.7:*
+ >=virtual/jre-1.8:*
sci-biology/samtools
sci-biology/picard
dev-db/sqlite:3"
diff --git a/sci-biology/tablet/tablet-9999.ebuild b/sci-biology/tablet/tablet-9999.ebuild
index d8aa02c19..f5846c8ef 100644
--- a/sci-biology/tablet/tablet-9999.ebuild
+++ b/sci-biology/tablet/tablet-9999.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
# $Id$
@@ -28,9 +28,9 @@ IUSE=""
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
- >=virtual/jdk-1.7:*"
+ >=virtual/jdk-1.8:*"
RDEPEND="${PYTHON_DEPS}
- >=virtual/jre-1.7:*
+ >=virtual/jre-1.8:*
sci-biology/samtools
sci-biology/picard
dev-db/sqlite:3"
@@ -44,6 +44,6 @@ src_install() {
java-pkg_dojar lib/scri-commons.jar
java-pkg_dojar lib/samtools*.jar
- echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
+ echo "PATH=${EPREFIX}/usr/share/${PN}" > 99Tablet
doenvd 99Tablet
}
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/tablet/
@ 2017-02-20 11:58 Martin Mokrejs
0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2017-02-20 11:58 UTC (permalink / raw
To: gentoo-commits
commit: f27be8844aa92e71587cdc83eb613a73eb73308f
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Feb 20 11:58:47 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Feb 20 11:58:47 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f27be884
sci-biology/tablet: do not zap 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-9999 as of now.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/tablet/tablet-1.15.09.01.ebuild | 21 +++++++++++----------
sci-biology/tablet/tablet-1.16.09.06.ebuild | 13 ++++++++-----
sci-biology/tablet/tablet-9999.ebuild | 13 ++++++++-----
3 files changed, 27 insertions(+), 20 deletions(-)
diff --git a/sci-biology/tablet/tablet-1.15.09.01.ebuild b/sci-biology/tablet/tablet-1.15.09.01.ebuild
index 2d30b71bb..17f7a5365 100644
--- a/sci-biology/tablet/tablet-1.15.09.01.ebuild
+++ b/sci-biology/tablet/tablet-1.15.09.01.ebuild
@@ -30,21 +30,22 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
>=virtual/jdk-1.8:*"
RDEPEND="${PYTHON_DEPS}
- >=virtual/jre-1.8:*
- sci-biology/samtools
- sci-biology/picard
- dev-db/sqlite:3"
+ >=virtual/jre-1.8:*"
+# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
+# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not sci-biology/samtools either
+# replacing picard.jar with a symlink to picard.jar from sci-biology.picard does not help either
S="${WORKDIR}"
src_install() {
- cd lib || die
- java-pkg_dojar tablet.jar
+ java-pkg_dojar lib/tablet.jar
java-pkg_dolauncher ${PN}
- java-pkg_dojar tablet-resources.jar
- java-pkg_dojar flamingo.jar
- java-pkg_dojar scri-commons.jar
- java-pkg_dojar samtools*.jar
+ java-pkg_dojar lib/tablet-resources.jar
+ java-pkg_dojar lib/flamingo.jar
+ java-pkg_dojar lib/scri-commons.jar
+ java-pkg_dojar lib/samtools*.jar
+ java-pkg_dojar lib/picard*.jar
+ java-pkg_dojar lib/sqlite-jdbc*.jar
echo "PATH=${EPREFIX}/usr/share/${PN}/" > 99Tablet
doenvd 99Tablet
diff --git a/sci-biology/tablet/tablet-1.16.09.06.ebuild b/sci-biology/tablet/tablet-1.16.09.06.ebuild
index c4be1406f..77f14a00f 100644
--- a/sci-biology/tablet/tablet-1.16.09.06.ebuild
+++ b/sci-biology/tablet/tablet-1.16.09.06.ebuild
@@ -30,19 +30,22 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
>=virtual/jdk-1.8:*"
RDEPEND="${PYTHON_DEPS}
- >=virtual/jre-1.8:*
- sci-biology/samtools
- sci-biology/picard
- dev-db/sqlite:3"
+ >=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_install() {
- java-pkg_dojar lib/tablet-resources.jar
java-pkg_dojar lib/tablet.jar
+ java-pkg_dolauncher ${PN}
+ java-pkg_dojar lib/tablet-resources.jar
java-pkg_dojar lib/flamingo.jar
java-pkg_dojar lib/scri-commons.jar
java-pkg_dojar lib/samtools*.jar
+ java-pkg_dojar lib/picard*.jar # is picard-1.113 in tablet-1.16.09.06
+ java-pkg_dojar lib/sqlite-jdbc*.jar
echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
doenvd 99Tablet
diff --git a/sci-biology/tablet/tablet-9999.ebuild b/sci-biology/tablet/tablet-9999.ebuild
index f5846c8ef..f137ea9ad 100644
--- a/sci-biology/tablet/tablet-9999.ebuild
+++ b/sci-biology/tablet/tablet-9999.ebuild
@@ -30,19 +30,22 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
>=virtual/jdk-1.8:*"
RDEPEND="${PYTHON_DEPS}
- >=virtual/jre-1.8:*
- sci-biology/samtools
- sci-biology/picard
- dev-db/sqlite:3"
+ >=virtual/jre-1.8:*"
+# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
+# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not sci-biology/samtools either
+# replacing picard.jar with a symlink to picard.jar from sci-biology.picard does not help either
S="${WORKDIR}"
src_install() {
- java-pkg_dojar lib/tablet-resources.jar
java-pkg_dojar lib/tablet.jar
+ java-pkg_dolauncher ${PN}
+ java-pkg_dojar lib/tablet-resources.jar
java-pkg_dojar lib/flamingo.jar
java-pkg_dojar lib/scri-commons.jar
java-pkg_dojar lib/samtools*.jar
+ java-pkg_dojar lib/picard*.jar
+ java-pkg_dojar lib/sqlite-jdbc*.jar
echo "PATH=${EPREFIX}/usr/share/${PN}" > 99Tablet
doenvd 99Tablet
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/tablet/
@ 2017-02-20 23:44 Martin Mokrejs
0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2017-02-20 23:44 UTC (permalink / raw
To: gentoo-commits
commit: bd5ac99eff210197a7c50c3a595c28f987f44a7f
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Feb 20 23:44:27 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Feb 20 23:44:27 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bd5ac99e
sci-biology/tablet: adding KEYWORDS to the latest release although building from SVN tag
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/tablet/tablet-1.16.09.06.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/tablet/tablet-1.16.09.06.ebuild b/sci-biology/tablet/tablet-1.16.09.06.ebuild
index 77f14a00f..f90f09bfb 100644
--- a/sci-biology/tablet/tablet-1.16.09.06.ebuild
+++ b/sci-biology/tablet/tablet-1.16.09.06.ebuild
@@ -18,7 +18,7 @@ if [ "$PV" == "9999" ]; then
KEYWORDS=""
else
ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
- KEYWORDS=""
+ KEYWORDS="~amd64 ~x86"
fi
LICENSE="Tablet"
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/tablet/
@ 2019-03-25 9:30 Martin Mokrejs
0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2019-03-25 9:30 UTC (permalink / raw
To: gentoo-commits
commit: b7d442c1ad60516bf1f2e25bdb4f7287ac29a0cd
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 25 09:30:16 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 25 09:30:16 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b7d442c1
sci-biology/tablet: update ebuild
New homepage, switch from svn to github, new license, switch
from picard to htsjdk
There is no ./classes/ so `ant build` does not work for me.
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
...-1.16.09.06.ebuild => tablet-1.17.08.17.ebuild} | 25 ++++++++++----------
sci-biology/tablet/tablet-9999.ebuild | 27 +++++++++++-----------
2 files changed, 25 insertions(+), 27 deletions(-)
diff --git a/sci-biology/tablet/tablet-1.16.09.06.ebuild b/sci-biology/tablet/tablet-1.17.08.17.ebuild
similarity index 63%
rename from sci-biology/tablet/tablet-1.16.09.06.ebuild
rename to sci-biology/tablet/tablet-1.17.08.17.ebuild
index e72339d61..08a272961 100644
--- a/sci-biology/tablet/tablet-1.16.09.06.ebuild
+++ b/sci-biology/tablet/tablet-1.17.08.17.ebuild
@@ -1,26 +1,25 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
PYTHON_COMPAT=( python2_7 )
inherit java-pkg-2 java-ant-2 python-r1
-# [ "$PV" == "9999" ] && inherit subversion
-inherit subversion
+[ "$PV" == "9999" ] && inherit git-r3
DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
+HOMEPAGE="https://ics.hutton.ac.uk/tablet"
if [ "$PV" == "9999" ]; then
- ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/"
+ EGIT_REPO_URI="https://github.com/cropgeeks/tablet.git"
KEYWORDS=""
else
- ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
- KEYWORDS="~amd64 ~x86"
+ SRC_URI="https://github.com/cropgeeks/tablet/archive/${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS=""
fi
-LICENSE="Tablet"
+LICENSE="BSD-2"
SLOT="0"
IUSE=""
@@ -29,10 +28,10 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
>=virtual/jdk-1.8:*"
RDEPEND="${PYTHON_DEPS}
- >=virtual/jre-1.8:*"
-# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
+ >=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
-# replacing picard.jar with a symlink to picard.jar from sci-biology.picard does not help either
S="${WORKDIR}"
@@ -43,7 +42,7 @@ src_install() {
java-pkg_dojar lib/flamingo.jar
java-pkg_dojar lib/scri-commons.jar
java-pkg_dojar lib/samtools*.jar
- java-pkg_dojar lib/picard*.jar # is picard-1.113 in tablet-1.16.09.06
+ java-pkg_dojar lib/htsjdk*.jar # is htsjdk-2.11.0 in tablet-1.17.08.17
java-pkg_dojar lib/sqlite-jdbc*.jar
echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
diff --git a/sci-biology/tablet/tablet-9999.ebuild b/sci-biology/tablet/tablet-9999.ebuild
index 467895e5d..01759c6b4 100644
--- a/sci-biology/tablet/tablet-9999.ebuild
+++ b/sci-biology/tablet/tablet-9999.ebuild
@@ -1,26 +1,25 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
PYTHON_COMPAT=( python2_7 )
inherit java-pkg-2 java-ant-2 python-r1
-# [ "$PV" == "9999" ] && inherit subversion
-inherit subversion
+[ "$PV" == "9999" ] && inherit git-r3
DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
+HOMEPAGE="https://ics.hutton.ac.uk/tablet"
if [ "$PV" == "9999" ]; then
- ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/"
+ EGIT_REPO_URI="https://github.com/cropgeeks/tablet.git"
KEYWORDS=""
else
- ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
+ SRC_URI="https://github.com/cropgeeks/tablet/archive/${PV}.tar.gz -> ${P}.tar.gz"
KEYWORDS=""
fi
-LICENSE="Tablet"
+LICENSE="BSD-2"
SLOT="0"
IUSE=""
@@ -29,12 +28,12 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="${PYTHON_DEPS}
>=virtual/jdk-1.8:*"
RDEPEND="${PYTHON_DEPS}
- >=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
+ >=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
-S="${WORKDIR}"
+#S="${WORKDIR}"
src_install() {
java-pkg_dojar lib/tablet.jar
@@ -43,7 +42,7 @@ src_install() {
java-pkg_dojar lib/flamingo.jar
java-pkg_dojar lib/scri-commons.jar
java-pkg_dojar lib/samtools*.jar
- java-pkg_dojar lib/picard*.jar
+ java-pkg_dojar lib/htsjdk*.jar
java-pkg_dojar lib/sqlite-jdbc*.jar
echo "PATH=${EPREFIX}/usr/share/${PN}" > 99Tablet
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/tablet/
@ 2019-03-25 9:30 Martin Mokrejs
0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2019-03-25 9:30 UTC (permalink / raw
To: gentoo-commits
commit: d54980d211f803108c958cd6b255827a0f9bd2a5
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 25 09:25:31 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 25 09:25:31 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d54980d2
sci-biology/tablet: drop old version
sci-biology/tablet/tablet-1.15.09.01.ebuild | 51 -----------------------------
1 file changed, 51 deletions(-)
diff --git a/sci-biology/tablet/tablet-1.15.09.01.ebuild b/sci-biology/tablet/tablet-1.15.09.01.ebuild
deleted file mode 100644
index c0b67d139..000000000
--- a/sci-biology/tablet/tablet-1.15.09.01.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit java-pkg-2 java-ant-2 python-r1
-
-# [ "$PV" == "9999" ] && inherit subversion
-inherit subversion
-
-DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
-if [ "$PV" == "9999" ]; then
- ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/"
- KEYWORDS=""
-else
- ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="Tablet"
-SLOT="0"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
- >=virtual/jdk-1.8:*"
-RDEPEND="${PYTHON_DEPS}
- >=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_install() {
- java-pkg_dojar lib/tablet.jar
- java-pkg_dolauncher ${PN}
- java-pkg_dojar lib/tablet-resources.jar
- java-pkg_dojar lib/flamingo.jar
- java-pkg_dojar lib/scri-commons.jar
- java-pkg_dojar lib/samtools*.jar
- java-pkg_dojar lib/picard*.jar
- java-pkg_dojar lib/sqlite-jdbc*.jar
-
- echo "PATH=${EPREFIX}/usr/share/${PN}/" > 99Tablet
- doenvd 99Tablet
-}
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/tablet/
@ 2019-03-25 11:56 Martin Mokrejs
0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2019-03-25 11:56 UTC (permalink / raw
To: gentoo-commits
commit: b7426d8f1df55eb09a50815dc95882363bb44895
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 25 11:56:28 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 25 11:56:28 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b7426d8f
sci-biology/tablet: still installs a mix of our and bundled jars
We have only dev-java/htdjdk-2.3.0 in the tree as newer versions
use gradle. The tablet-1.17.08.17 lacks the lib/htsjdk-2.0.11.jar
so we cannot install it. Use sci-biology/tablet-bin instead.
https://github.com/cropgeeks/tablet/issues/6
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/tablet/tablet-1.17.08.17.ebuild | 29 +++++++++++++++++++++--------
sci-biology/tablet/tablet-9999.ebuild | 17 ++++++++++++++---
2 files changed, 35 insertions(+), 11 deletions(-)
diff --git a/sci-biology/tablet/tablet-1.17.08.17.ebuild b/sci-biology/tablet/tablet-1.17.08.17.ebuild
index 08a272961..158caba78 100644
--- a/sci-biology/tablet/tablet-1.17.08.17.ebuild
+++ b/sci-biology/tablet/tablet-1.17.08.17.ebuild
@@ -16,7 +16,7 @@ if [ "$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/${PN}" > 99Tablet
^ permalink raw reply related [flat|nested] 11+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/tablet/
@ 2019-03-28 22:06 Martin Mokrejs
0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2019-03-28 22:06 UTC (permalink / raw
To: gentoo-commits
commit: 6ff12313344e3b1b686430875f4b866c67ab8d4f
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 28 22:06:49 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 28 22:06:49 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6ff12313
sci-biology/tablet: fix indentation
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/tablet/tablet-9999.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/tablet/tablet-9999.ebuild b/sci-biology/tablet/tablet-9999.ebuild
index 5cebde785..e9ae6890d 100644
--- a/sci-biology/tablet/tablet-9999.ebuild
+++ b/sci-biology/tablet/tablet-9999.ebuild
@@ -51,7 +51,7 @@ src_install() {
java-pkg_dojar lib/samtools-linux64.jar
fi
if [ "${ABI}" == "x86" ]; then
- java-pkg_dojar lib/samtools-linux32.jar
+ 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
^ permalink raw reply related [flat|nested] 11+ messages in thread
end of thread, other threads:[~2019-03-28 22:06 UTC | newest]
Thread overview: 11+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2015-02-18 16:41 [gentoo-commits] proj/sci:master commit in: sci-biology/tablet/ Justin Lecher
-- strict thread matches above, loose matches on Subject: below --
2019-03-28 22:06 Martin Mokrejs
2019-03-25 11:56 Martin Mokrejs
2019-03-25 9:30 Martin Mokrejs
2019-03-25 9:30 Martin Mokrejs
2017-02-20 23:44 Martin Mokrejs
2017-02-20 11:58 Martin Mokrejs
2017-02-19 0:54 Martin Mokrejs
2015-02-18 16:41 Justin Lecher
2015-01-09 15:35 Martin Mokrejs
2014-07-02 22:42 Martin Mokrejs
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox