From 03e6391c2d30887d78676f50bf050a121a5b6da4 Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Wed, 20 Apr 2016 21:05:03 +0200 Subject: sci-biology/tablet-bin: version bump; added coveragestats.py (requires dos2unix) Package-Manager: portage-2.2.28 --- sci-biology/tablet-bin/Manifest | 2 +- .../tablet-bin/tablet-bin-1.14.10.21.ebuild | 97 -------------------- .../tablet-bin/tablet-bin-1.15.09.01.ebuild | 101 +++++++++++++++++++++ 3 files changed, 102 insertions(+), 98 deletions(-) delete mode 100644 sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild create mode 100644 sci-biology/tablet-bin/tablet-bin-1.15.09.01.ebuild (limited to 'sci-biology/tablet-bin') diff --git a/sci-biology/tablet-bin/Manifest b/sci-biology/tablet-bin/Manifest index fbb7986d1..d58ee461e 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-1.14.10.21.sh 44245815 SHA256 3e949fdb3610bce2c5e3db932cacdc6848d46a67240769ac136d790f789dd294 SHA512 2ded1c11e98232a82d34b813903bf52606c245f34a6eab0392e90947ea03885e4010ecfb784d60260a81356d08c38e4be5d3050e3d98b2565c4ad6b98b960c86 WHIRLPOOL 318dca0899b25b3acd64cbb92d5400983020477c721b379ebb219ac2e54c597408d7822ef9102c844a1e4fb0d4d7dd639869def11efa075b9be07f844dc47ac6 +DIST tablet-bin-1.15.09.01.sh 45846642 SHA256 8f1f74b69fd2f27b66f01d81c28d73d382f179b8e8b9079094c30f0e081c50c3 SHA512 fb75fbff7c08e0271fcba83ee9ec85d67e5cff698f8520c227a02d80635f4003bc70449389d1bb4aacdfab85825805948fcc9f0b526936d0b1877359ed69e365 WHIRLPOOL 6e45f4259c93ee8d22da921a18f5bc9e4b9d53ffd7afb6b1409bd89c5473d2ffd09a0e6bfe8d3309694ee236f86f1761fb94a8c8767b5aa677e964aa2d4ee7df diff --git a/sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild b/sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild deleted file mode 100644 index 6c0e63a2b..000000000 --- a/sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild +++ /dev/null @@ -1,97 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit java-pkg-2 python-r1 - -DESCRIPTION="Viewer of next generation sequence assemblies and alignments" -HOMEPAGE="http://ics.hutton.ac.uk/tablet/" -SRC_URI=" - 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 -> ${P}.sh ) - http://bioinf.hutton.ac.uk/tablet/additional/coveragestats.py" - -# Upstream says regarding source code unavailability: -# Tablet uses a modified version of the BSD License which has been edited to -# remove references to distribution and use in source forms. This means that -# we are happy for you to distribute and use Tablet however you please, but we -# do not (yet) want to make the source code publicly available. - -# The licence file itself is in the installer, and ends up on disk after -# installation at /opt/Tablet/docs/tablet.html -# The original BSD licence was modified to remove references to distribution -# and use in source forms, because we cannot make the source code available -# for Tablet. - -LICENSE="Tablet" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -REQUIRED_USE="${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 -} diff --git a/sci-biology/tablet-bin/tablet-bin-1.15.09.01.ebuild b/sci-biology/tablet-bin/tablet-bin-1.15.09.01.ebuild new file mode 100644 index 000000000..d894aa183 --- /dev/null +++ b/sci-biology/tablet-bin/tablet-bin-1.15.09.01.ebuild @@ -0,0 +1,101 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit java-pkg-2 python-r1 + +DESCRIPTION="Viewer of next generation sequence assemblies and alignments" +HOMEPAGE="http://ics.hutton.ac.uk/tablet/" +SRC_URI=" + 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 -> ${P}.sh ) + http://bioinf.hutton.ac.uk/tablet/additional/coveragestats.py" + +# Upstream says regarding source code unavailability: +# Tablet uses a modified version of the BSD License which has been edited to +# remove references to distribution and use in source forms. This means that +# we are happy for you to distribute and use Tablet however you please, but we +# do not (yet) want to make the source code publicly available. + +# The licence file itself is in the installer, and ends up on disk after +# installation at /opt/Tablet/docs/tablet.html +# The original BSD licence was modified to remove references to distribution +# and use in source forms, because we cannot make the source code available +# for Tablet. + +LICENSE="Tablet" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND="${PYTHON_DEPS} + app-text/dos2unix" +RDEPEND="${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 "${WORKDIR}"/coveragestats.py + dos2unix "${WORKDIR}"/coveragestats.py coveragestats.py || die + insinto /opt/Tablet/utils + doins coveragestats.py + + echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet + doenvd 99Tablet +} -- cgit v1.2.3-65-gdbad