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Diffstat (limited to 'sci-biology/tablet-bin/tablet-bin-1.11.02.18.ebuild')
| -rw-r--r-- | sci-biology/tablet-bin/tablet-bin-1.11.02.18.ebuild | 59 |
1 files changed, 59 insertions, 0 deletions
diff --git a/sci-biology/tablet-bin/tablet-bin-1.11.02.18.ebuild b/sci-biology/tablet-bin/tablet-bin-1.11.02.18.ebuild new file mode 100644 index 000000000..d4b19252c --- /dev/null +++ b/sci-biology/tablet-bin/tablet-bin-1.11.02.18.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +inherit python java-pkg-2 + +DESCRIPTION="Graphical viewer for 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_1_11_02_18.sh + http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py" + +# 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. + +# It's 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="" + +DEPEND="" +RDEPEND="${DEPEND} + virtual/jre + dev-lang/python" + +src_install() { + # In theory it seems this binary package could be installed through ant instead + # of the install4j package which is not easy to be forced non-interactive. + # The below approach is not ideal. + sed "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile > "${DISTDIR}"/response.varfile || die "sed failed" + + # the intallation script somehow does not pickup + # -varfile="${DISTDIR}"/response.varfile from the commandline and tehrefore + # we place the file rather directly into the place where it should reside. + # In the file you can read details how the variables were mangled. For + # example, the trick with sys.symlinkDir in the response.varfile is to + # disable the installation process to symlink from /usr/local/bin/table to + # /opt/Tablet/tablet. That was logged in that file with the following line: + # + # /scratch/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log: Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String] + # + # The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile + mkdir -p "${D}"/opt/Tablet/.install4j || die "Cannot pre-create "${D}"/opt/Tablet/.install4j/" + cat "${DISTDIR}"/response.varfile > "${D}"/opt/Tablet/.install4j/response.varfile || die "Cannot write "${D}"/opt/Tablet/.install4j/response.varfile" + + # make sure we force java to point a to $HOME which is inside our sanbox + # directory area. We force -Duser.home . It seems also -Dinstall4j.userHome + # could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/ + sed "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${D}"/../temp -Dinstall4j.jvmDir#" -i "${DISTDIR}"/tablet_linux_x86_1_11_02_18.sh || die "failed to set userHome value" + sh "${DISTDIR}"/tablet_linux_x86_1_11_02_18.sh -q -overwrite -varfile="${DISTDIR}"/response.varfile --destination="${D}"/opt/Tablet -dir /scratch/var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet + dobin "${DISTDIR}"/coveragestats.py +} |