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

["Justin Lecher" <jlec@gentoo.org>]

commit:     0a5a7511e618764600d35bd6d03c08b1ecf7f0f9
Author:     Ted Tanberry <ted.tanberry <AT> gmail <DOT> com>
AuthorDate: Sun Mar 15 18:17:50 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar 15 18:17:50 2015 +0000
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 <ted.tanberry@gmail.com>
+  +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 <ottxor@gentoo.org>
   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..0000000
--- 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 $HOME which is inside our sanbox
-	# directory area. We force -Duser.home . It seems also -Dinstall4j.userHome
-	# could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/
-	sed \
-		-e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${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
-
-	python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
-
-	echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
-	doenvd 99Tablet || die
-}

diff --git a/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild b/sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild
similarity index 91%
rename from sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild
rename to sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild
index d13ad0c..4f36d7e 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.14.10.21.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: $
 
@@ -11,9 +11,9 @@ 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 -> ${P}.sh )
-	http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
+	x86? ( http://bioinf.hutton.ac.uk/tablet/installers/tablet_linux_x86_$(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 )
+	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