diff options
| -rw-r--r-- | sci-biology/staden-bin/ChangeLog | 10 | ||||
| -rw-r--r-- | sci-biology/staden-bin/Manifest | 16 | ||||
| -rw-r--r-- | sci-biology/staden-bin/files/digest-staden-bin-1.7.0 | 3 | ||||
| -rw-r--r-- | sci-biology/staden-bin/metadata.xml | 9 | ||||
| -rw-r--r-- | sci-biology/staden-bin/staden-bin-1.7.0.ebuild | 93 |
5 files changed, 131 insertions, 0 deletions
diff --git a/sci-biology/staden-bin/ChangeLog b/sci-biology/staden-bin/ChangeLog new file mode 100644 index 000000000000..7b36f8386a81 --- /dev/null +++ b/sci-biology/staden-bin/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/staden-bin +# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden-bin/ChangeLog,v 1.1 2006/10/22 16:37:35 ribosome Exp $ + +*staden-bin-1.7.0 (22 Oct 2006) + + 22 Oct 2006; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, + +staden-bin-1.7.0.ebuild: + Initial import. + diff --git a/sci-biology/staden-bin/Manifest b/sci-biology/staden-bin/Manifest new file mode 100644 index 000000000000..bd908afbae45 --- /dev/null +++ b/sci-biology/staden-bin/Manifest @@ -0,0 +1,16 @@ +DIST staden-linux-x86-1-7-0.tar.gz 38515727 RMD160 99dd575a9682719cdd8cff35dbd13c5073c61b32 SHA1 31014bb1a453b024fd4e969664da5acf6f7fc169 SHA256 38c96b2df886ebb2407e21bd3c0059d632c2db9a6a7ab707f31c90f6db9e5e0e +EBUILD staden-bin-1.7.0.ebuild 2951 RMD160 35332b0d0aacaf0e7e780e262106bc2cefe69bcd SHA1 ae6b31c6508cfdecd011a90a44b6dfd1f04b36c1 SHA256 8138a52b2c7fcb1cefff1c9ff55a7174200f19249605ea126c76b5948e3e80e8 +MD5 8b1b9a974d31a2e7e5d843b317bad1f6 staden-bin-1.7.0.ebuild 2951 +RMD160 35332b0d0aacaf0e7e780e262106bc2cefe69bcd staden-bin-1.7.0.ebuild 2951 +SHA256 8138a52b2c7fcb1cefff1c9ff55a7174200f19249605ea126c76b5948e3e80e8 staden-bin-1.7.0.ebuild 2951 +MISC ChangeLog 271 RMD160 af53e912e40af561f5ea29f9dd1a2b9dbaa31099 SHA1 018478eb60b530ca99c0092f228a854dd5bb7349 SHA256 b69d4a37d9a0e3804ee26ffc8f29b8fdbe197080b103c3792817ad7d69c68c77 +MD5 e77acce226eaa2474d20084fefc339d3 ChangeLog 271 +RMD160 af53e912e40af561f5ea29f9dd1a2b9dbaa31099 ChangeLog 271 +SHA256 b69d4a37d9a0e3804ee26ffc8f29b8fdbe197080b103c3792817ad7d69c68c77 ChangeLog 271 +MISC metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 SHA1 3c024ca60a2b93ed0e0311f6b05ef5ef117bee31 SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f +MD5 5f35ae4b4cb1cd144db7c7c093d3fd80 metadata.xml 262 +RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 metadata.xml 262 +SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f metadata.xml 262 +MD5 da06914b2f9e2bb9617639db1578c5e4 files/digest-staden-bin-1.7.0 274 +RMD160 20d65fe0e81a5feed63f41e2925108ab088edf44 files/digest-staden-bin-1.7.0 274 +SHA256 022e1e0c801b0084bd0293706997f38a28fdbd929e83276e12d20ae4711a7a4f files/digest-staden-bin-1.7.0 274 diff --git a/sci-biology/staden-bin/files/digest-staden-bin-1.7.0 b/sci-biology/staden-bin/files/digest-staden-bin-1.7.0 new file mode 100644 index 000000000000..42feae6f3546 --- /dev/null +++ b/sci-biology/staden-bin/files/digest-staden-bin-1.7.0 @@ -0,0 +1,3 @@ +MD5 57edef52b055c42fbef307673e844677 staden-linux-x86-1-7-0.tar.gz 38515727 +RMD160 99dd575a9682719cdd8cff35dbd13c5073c61b32 staden-linux-x86-1-7-0.tar.gz 38515727 +SHA256 38c96b2df886ebb2407e21bd3c0059d632c2db9a6a7ab707f31c90f6db9e5e0e staden-linux-x86-1-7-0.tar.gz 38515727 diff --git a/sci-biology/staden-bin/metadata.xml b/sci-biology/staden-bin/metadata.xml new file mode 100644 index 000000000000..ebbff811d3b4 --- /dev/null +++ b/sci-biology/staden-bin/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>ribosome@gentoo.org</email> + <name>Olivier Fisette</name> + </maintainer> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/staden-bin/staden-bin-1.7.0.ebuild b/sci-biology/staden-bin/staden-bin-1.7.0.ebuild new file mode 100644 index 000000000000..09b51b987431 --- /dev/null +++ b/sci-biology/staden-bin/staden-bin-1.7.0.ebuild @@ -0,0 +1,93 @@ +# Copyright 1999-2006 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/staden-bin/staden-bin-1.7.0.ebuild,v 1.1 2006/10/22 16:37:35 ribosome Exp $ + +inherit multilib + +DESCRIPTION="The Staden Package - Biological sequence handling and analysis" +LICENSE="staden" +HOMEPAGE="http://staden.sourceforge.net" +SRC_URI="mirror://sourceforge/staden/staden-linux-x86-${PV//./-}.tar.gz" + +SLOT="0" +IUSE="" +KEYWORDS="~x86" + +ITCLTK_PV="3.3" +IWIDGETS_PV="4.0.1" + +RDEPEND="app-shells/pdksh + =media-libs/libpng-1.2* + =sci-libs/io_lib-1.10* + ~dev-tcltk/itcl-${ITCLTK_PV} + ~dev-tcltk/itk-${ITCLTK_PV} + ~dev-tcltk/iwidgets-${IWIDGETS_PV} + x11-libs/libX11" + +S="${WORKDIR}/staden-linux-x86-${PV//./-}" + +src_unpack() { + unpack ${A} + cd "${S}" + + # Remove Gentoo-provided libraries. + rm lib/linux-binaries/libpng* || die "Could not remove libpng." + rm -r lib/itcl${ITCLTK_PV} || die "Could not remove itcl." + rm -r lib/itk${ITCLTK_PV} || die "Could not remove itk." + rm lib/iwidgets || die "Could not remove iwidgets." + + # Remove executables provided by the io_lib package. + for i in append_sff convert_trace extract_seq get_comment hash_extract \ + hash_sff hash_tar index_tar makeSCF scf_dump scf_info scf_update \ + trace_dump ztr_dump; do + rm linux-bin/${i} || die "Could not remove io_lib program: ${i}." + done + + # Remove the help program, which is only a wrapper to launch netscape + # with a non-existent hypertext file. + rm linux-bin/staden_help || die "Could not remove staden-help." + + # Remove broken prebuilt EMBOSS tcl/tk GUIs. + rm tables/emboss_menu + rm -r lib/spin_emboss/acdtcl + rm -r lib/spin2_emboss/acdtcl + + sed -e 's:/usr/bin/nawk:/usr/bin/awk:' -i linux-bin/fasta-split || \ + die "Could not patch fasta-split." + sed -e 's:/usr/local/badger/gap4_test:/opt/staden:' \ + -i linux-bin/finish_cDNA -i linux-bin/finish_cDNA_ends_only || \ + die "Could not patch finish_cDNA" +} + +src_compile() { + echo; einfo "Nothing to compile"; echo +} + +src_install() { + # There is no Makefile. + dodir /opt/staden + cp -R "${S}"/* "${D}"/opt/staden/ || die "Could not copy package files." + dosym /opt/staden/doc /usr/share/doc/${PF} || die "Could not symlink docs." + + # Staden programs look for the tcl/tk/itcl/itk/iwidgets libraries in the + # package root. + dosym /usr/$(get_libdir)/itcl${ITCLTK_PV} /opt/staden/lib/itcl${ITCLTK_PV} \ + || die "Could not symlink itcl." + dosym /usr/$(get_libdir)/itk${ITCLTK_PV} /opt/staden/lib/itk${ITCLTK_PV} \ + || die "Could not symlink itk." + dosym /usr/$(get_libdir)/iwidgets${IWIDGETS_PV} /opt/staden/lib/iwidgets \ + || die "Could not symlink iwidgets." + + dodir /etc/env.d + cat <<- EOF > "${D}"/etc/env.d/60staden + STADENROOT="/opt/staden" + EOF +} + +pkg_postinst() { + echo + einfo "Before using Staden applications, csh users should source" + einfo "\"/opt/staden/staden.login\", whilst bash users should source" + einfo "\"/opt/staden/staden.profile\"." + echo +} |