From mboxrd@z Thu Jan 1 00:00:00 1970
Return-Path: <gentoo-commits+bounces-708328-garchives=archives.gentoo.org@lists.gentoo.org>
Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80])
by finch.gentoo.org (Postfix) with ESMTP id B426313877A
for <garchives@archives.gentoo.org>; Wed, 2 Jul 2014 22:42:53 +0000 (UTC)
Received: from pigeon.gentoo.org (localhost [127.0.0.1])
by pigeon.gentoo.org (Postfix) with SMTP id 058BCE0827;
Wed, 2 Jul 2014 22:42:53 +0000 (UTC)
Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183])
(using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits))
(No client certificate requested)
by pigeon.gentoo.org (Postfix) with ESMTPS id 70F35E0827
for <gentoo-commits@lists.gentoo.org>; Wed, 2 Jul 2014 22:42:52 +0000 (UTC)
Received: from spoonbill.gentoo.org (spoonbill.gentoo.org [81.93.255.5])
(using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits))
(No client certificate requested)
by smtp.gentoo.org (Postfix) with ESMTPS id 18E7E33FED9
for <gentoo-commits@lists.gentoo.org>; Wed, 2 Jul 2014 22:42:51 +0000 (UTC)
Received: from localhost.localdomain (localhost [127.0.0.1])
by spoonbill.gentoo.org (Postfix) with ESMTP id DC7A6193E5
for <gentoo-commits@lists.gentoo.org>; Wed, 2 Jul 2014 22:42:49 +0000 (UTC)
From: "Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>
To: gentoo-commits@lists.gentoo.org
Content-Transfer-Encoding: 8bit
Content-type: text/plain; charset=UTF-8
Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>
Message-ID: <1404340849.01ff3a2d6b36716aa83e749acfeb4cc09e076ba8.mmokrejs@gentoo>
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
X-VCS-Repository: proj/sci
X-VCS-Files: sci-biology/tablet-bin/ChangeLog sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild
X-VCS-Directories: sci-biology/tablet-bin/
X-VCS-Committer: mmokrejs
X-VCS-Committer-Name: Martin Mokrejs
X-VCS-Revision: 01ff3a2d6b36716aa83e749acfeb4cc09e076ba8
X-VCS-Branch: master
Date: Wed, 2 Jul 2014 22:42:49 +0000 (UTC)
Precedence: bulk
List-Post: <mailto:gentoo-commits@lists.gentoo.org>
List-Help: <mailto:gentoo-commits+help@lists.gentoo.org>
List-Unsubscribe: <mailto:gentoo-commits+unsubscribe@lists.gentoo.org>
List-Subscribe: <mailto:gentoo-commits+subscribe@lists.gentoo.org>
List-Id: Gentoo Linux mail <gentoo-commits.gentoo.org>
X-BeenThere: gentoo-commits@lists.gentoo.org
X-Archives-Salt: e9f7bc86-9699-4efa-b62d-55d355e11dd5
X-Archives-Hash: 3d692dc0660e381228875465714abd7c
commit: 01ff3a2d6b36716aa83e749acfeb4cc09e076ba8
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jul 2 22:40:49 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jul 2 22:40:49 2014 +0000
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 <mmokrejs@fold.natur.cuni.cz>
+ +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 <mmokrejs@fold.natur.cuni.cz>
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 0000000..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 \
+ -varfile="${DISTDIR}"/response.varfile \
+ --destination="${ED}"/opt/Tablet \
+ -dir "${ED}"/opt/Tablet || die
+
+ rm -rf "${ED}"/opt/Tablet/jre || 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
+ # * The file has incompatible shebang:
+ # * file: /usr/lib/python-exec/python2.7/coveragestats.py
+ # * current shebang: #!/usr/bin/env python
+ # * requested impl: python2.7
+ #
+ # python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
+
+ echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
+ doenvd 99Tablet || die
+}