From f50f465dae726ce192266930b570a8a6ab296a89 Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Mon, 20 Jan 2014 22:19:29 +0100 Subject: Version bump Package-Manager: portage-2.2.7 --- sci-biology/tablet-bin/ChangeLog | 9 ++- sci-biology/tablet-bin/Manifest | 2 +- .../tablet-bin/tablet-bin-1.13.05.17.ebuild | 89 --------------------- .../tablet-bin/tablet-bin-1.13.12.17.ebuild | 90 ++++++++++++++++++++++ 4 files changed, 98 insertions(+), 92 deletions(-) delete mode 100644 sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild create mode 100644 sci-biology/tablet-bin/tablet-bin-1.13.12.17.ebuild diff --git a/sci-biology/tablet-bin/ChangeLog b/sci-biology/tablet-bin/ChangeLog index b41197884..d48473ae8 100644 --- a/sci-biology/tablet-bin/ChangeLog +++ b/sci-biology/tablet-bin/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-biology/tablet-bin -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*tablet-bin-1.13.12.17 (20 Jan 2014) + + 20 Jan 2014; Martin Mokrejs + +tablet-bin-1.13.12.17.ebuild, -tablet-bin-1.13.05.17.ebuild: + Version bump + 16 Jun 2013; Justin Lecher tablet-bin-1.13.05.17.ebuild: Version Bump; Bump to EAPI5 and python-r1.eclass; drop addpredict @@ -31,4 +37,3 @@ 09 Dec 2011; Martin Mokrejs tablet-bin-1.11.05.03.ebuild, +tablet-bin-1.11.11.01.ebuild: ebuild cleanup, version bump - diff --git a/sci-biology/tablet-bin/Manifest b/sci-biology/tablet-bin/Manifest index 18833160e..ae1e4a6af 100644 --- a/sci-biology/tablet-bin/Manifest +++ b/sci-biology/tablet-bin/Manifest @@ -1,2 +1,2 @@ DIST coveragestats.py 4800 SHA256 358b686d00fd75d2cc9af490b0e7d635f74cbb1c0b153df22d8ff879884d47bc SHA512 d5688832c13dc9c2e2e015df0b5c50113f72e2eeae076d479c43b65a4b028f8dcfa5f0fb833b4341d76d3956ea27707c55a51389b73a2efed6abd2b96ccdc3cd WHIRLPOOL 0b1eb20189b343d6014097748c053f35f8ad162400312cfbde16bac7fee52f24ac8b0055e991c823dcb64d7a20df3fbb88d8cd6119f838d4e9a5f26e82604664 -DIST tablet-bin-1.13.05.17.sh 35467547 SHA256 6da2cbb8d15433cdf022c93f466d355515a9c1c8f89dcdab4c2e9543bee415e4 SHA512 532900242ef3b3a46a6e6379c29b627c9f337198cf230273eb1da4c269b6f09a49bc7c5ea28a1ee4caa4f7d7a76ba0e0f18330a538428e49b8f1d36c3bfecb78 WHIRLPOOL 299f23da5f6192a7802f86e61e2c5655711d0d672e28cdd257fdd179d76e15e1b951fa42ec2b28e4568063197b14e1884d61992b7ff2e864fa86c3dad2141c14 +DIST tablet-bin-1.13.12.17.sh 34395356 SHA256 fab481dd2a19e1c25142c41e75c483eeac36cc6793921a2643d9472f0aecbd2b SHA512 6fee28fd68ac4dde777dc7b873735e165d19bec47997a49185f21eecaaf2f38ca019b5af30ff18177ed69ad01eb8a797ef8b892631780ad548bf8fdf3ceb2f0b WHIRLPOOL 274e3849096179707af5ad36001ba060b5c5be068350454553997a120ec5c5f33b347ea26f3f9bd356bb7191b1c1e07199a6f6c0073e5b7edb7bf953d46c0974 diff --git a/sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild b/sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild deleted file mode 100644 index 762e888aa..000000000 --- a/sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild +++ /dev/null @@ -1,89 +0,0 @@ -# Copyright 1999-2013 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=" - http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(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-1.13.12.17.ebuild b/sci-biology/tablet-bin/tablet-bin-1.13.12.17.ebuild new file mode 100644 index 000000000..7b7d0013a --- /dev/null +++ b/sci-biology/tablet-bin/tablet-bin-1.13.12.17.ebuild @@ -0,0 +1,90 @@ +# 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 +} -- cgit v1.2.3-65-gdbad