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

5 files changed, 96 insertions, 127 deletions

diff --git a/sci-biology/tablet/ChangeLog b/sci-biology/tablet/ChangeLog
index 0080ef21c..0cca8d837 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/Manifest b/sci-biology/tablet/Manifest
deleted file mode 100644
index 05da7e849..000000000
--- a/sci-biology/tablet/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST coveragestats.py 4800 SHA256 358b686d00fd75d2cc9af490b0e7d635f74cbb1c0b153df22d8ff879884d47bc SHA512 d5688832c13dc9c2e2e015df0b5c50113f72e2eeae076d479c43b65a4b028f8dcfa5f0fb833b4341d76d3956ea27707c55a51389b73a2efed6abd2b96ccdc3cd WHIRLPOOL 0b1eb20189b343d6014097748c053f35f8ad162400312cfbde16bac7fee52f24ac8b0055e991c823dcb64d7a20df3fbb88d8cd6119f838d4e9a5f26e82604664
-DIST tablet-1.13.12.17.sh 34395356 SHA256 fab481dd2a19e1c25142c41e75c483eeac36cc6793921a2643d9472f0aecbd2b SHA512 6fee28fd68ac4dde777dc7b873735e165d19bec47997a49185f21eecaaf2f38ca019b5af30ff18177ed69ad01eb8a797ef8b892631780ad548bf8fdf3ceb2f0b WHIRLPOOL 274e3849096179707af5ad36001ba060b5c5be068350454553997a120ec5c5f33b347ea26f3f9bd356bb7191b1c1e07199a6f6c0073e5b7edb7bf953d46c0974
diff --git a/sci-biology/tablet/tablet-1.13.12.17.ebuild b/sci-biology/tablet/tablet-1.13.12.17.ebuild
index 112709b08..1940cb9c7 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 000000000..1940cb9c7
--- /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 40472c753..1940cb9c7 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