From 990d1b8b1de49d714405f9824eccef0fd08c3f35 Mon Sep 17 00:00:00 2001 From: Andrey Kislyuk Date: Sun, 15 Mar 2009 16:58:21 +0000 Subject: Revision bump fixes several issues in installation of supplementary files Package-Manager: portage-2.2_rc20/cvs/Linux 2.6.26-gentoo-r4 x86_64 --- sci-biology/consed/ChangeLog | 8 +++- sci-biology/consed/Manifest | 4 +- sci-biology/consed/consed-19-r1.ebuild | 70 ++++++++++++++++++++++++++++++++++ sci-biology/consed/consed-19.ebuild | 57 --------------------------- 4 files changed, 79 insertions(+), 60 deletions(-) create mode 100644 sci-biology/consed/consed-19-r1.ebuild delete mode 100644 sci-biology/consed/consed-19.ebuild (limited to 'sci-biology/consed') diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog index 3ba58f774c4c..26f4f2b2ad8a 100644 --- a/sci-biology/consed/ChangeLog +++ b/sci-biology/consed/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-biology/consed # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.1 2009/02/18 16:21:44 weaver Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.2 2009/03/15 16:58:21 weaver Exp $ + +*consed-19-r1 (15 Mar 2009) + + 15 Mar 2009; Andrey Kislyuk -consed-19.ebuild, + +consed-19-r1.ebuild: + Revision bump fixes several issues in installation of supplementary files *consed-19 (18 Feb 2009) diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest index b3f01946d69e..aae40fabcc0b 100644 --- a/sci-biology/consed/Manifest +++ b/sci-biology/consed/Manifest @@ -1,5 +1,5 @@ DIST consed-19-linux.tar.gz 29835559 RMD160 06765fe4beee2bb8f1f72b7cb9522acadf8df1d3 SHA1 7b01affde92cda6ff0bcb49199ed6c7e60b044d5 SHA256 27501d714e4cd7ea04def6a7f985b674bc454ed8bd7d1e86b41b0283e2b9e089 DIST consed-19-sources.tar.gz 6867357 RMD160 52bb03197a75827214b30c8ce833d9479fc9aa63 SHA1 ee40c48b887fc457c869b0d997ca650a0a7864af SHA256 1db37b17608e49470926dae261c76d400cf3f9eb5feea52cd732e0bfa4cadee3 -EBUILD consed-19.ebuild 1798 RMD160 e4e94ae5197232f70743e0d3818e7b55ca6bd83a SHA1 596ef69ecec6ca631fba6b6f8d4605f3dcf1f565 SHA256 e334fea21b68680a55b6b61da6e1b80cb9005616fc7551fe36616a3a2387ed3c -MISC ChangeLog 435 RMD160 08ac7abec8febb64edbb4f4f8112d7413b5cb7c9 SHA1 ea9e5f68264b09f73a3a85695bee4e63c9b60f0a SHA256 0e90f68c90e1d454f4c1843ec0fda9fac132932960894543c6125dfb39cfef66 +EBUILD consed-19-r1.ebuild 2293 RMD160 4c854f458baf43e9eb2928fc3a9076a5a4b6f42c SHA1 2a2e523f5d8ce67d82752d7a433ce93fbd352f42 SHA256 e521dd9ab4a1ac067f28e4201522be60a2ca0e71a12c7b108b22a1a3bfffc634 +MISC ChangeLog 634 RMD160 c1a3f3f391aca73a02f7762e458993fb6b8acd29 SHA1 f0c505ecf73f87fb1bd241af53d48c2575070a84 SHA256 6351b7699ebd3ce54c45a00cec56bd09a266fffb07306427c0285a49f37056f1 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110 diff --git a/sci-biology/consed/consed-19-r1.ebuild b/sci-biology/consed/consed-19-r1.ebuild new file mode 100644 index 000000000000..168e97a9fe72 --- /dev/null +++ b/sci-biology/consed/consed-19-r1.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild,v 1.1 2009/03/15 16:58:21 weaver Exp $ + +inherit toolchain-funcs + +DESCRIPTION="Consed: a genome sequence finishing program" +HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" +SRC_URI="${P}-sources.tar.gz + ${P}-linux.tar.gz" + +LICENSE="phrap" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="" + +DEPEND="x11-libs/openmotif" +RDEPEND="${DEPEND} + >=sci-biology/phred-000925 + >=sci-biology/phrap-1.080721" + +S="${WORKDIR}" + +RESTRICT="fetch" + +pkg_nofetch() { + einfo "Please visit ${HOMEPAGE} and obtain the file" + einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" + einfo "and place it in ${DISTDIR}," + einfo "obtain the file" + einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" + einfo "and place it in ${DISTDIR}" +} + +src_unpack() { + unpack ${A} + sed -i '/#include/ s///' "${S}/main.cpp" || die + sed -i -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm/' \ + -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ + -e 's/CFLGS=/CFLGS= ${CFLAGS} /' "${S}/makefile" || die + sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die + sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die +} + +src_compile() { + emake || die + emake -C misc/mktrace || die + emake -C misc/phd2fasta || die + (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die +} + +src_install() { + dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die + dobin scripts/* contributions/* || die + insinto /usr/lib/screenLibs + doins misc/*.{fa*,seq} + insinto /usr/share/${PN}/examples + doins -r standard polyphred autofinish assembly_view 454_newbler \ + align454reads align454reads_answer solexa_example \ + solexa_example_answer selectRegions selectRegionsAnswer || die + echo 'CONSED_HOME=/usr' > "${S}/99consed" + echo 'PHRED_PARAMETER_FILE=/usr/share/phred/phredpar.dat' >> "${S}/99consed" + doenvd "${S}/99consed" || die + dodoc README.txt *_announcement.txt +} + +pkg_postinst() { + einfo "Package documentation is available at" + einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt" +} diff --git a/sci-biology/consed/consed-19.ebuild b/sci-biology/consed/consed-19.ebuild deleted file mode 100644 index 85e6a7e209e0..000000000000 --- a/sci-biology/consed/consed-19.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19.ebuild,v 1.1 2009/02/18 16:21:44 weaver Exp $ - -inherit toolchain-funcs - -DESCRIPTION="Consed: a genome sequence finishing program" -HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html" -SRC_URI="consed-19-sources.tar.gz - consed-19-linux.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="" - -DEPEND="x11-libs/openmotif" -RDEPEND="${DEPEND} - >=sci-biology/phrap-1.080721" - -S="${WORKDIR}" - -RESTRICT="fetch" - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "\"sources.tar.gz\", then rename it to \"consed-${PV}-sources.tar.gz\"" - einfo "and place it in ${DISTDIR}," - einfo "obtain the file" - einfo "\"consed_linux.tar.gz\", then rename it to \"consed-${PV}-linux.tar.gz\"" - einfo "and place it in ${DISTDIR}" -} - -src_unpack() { - unpack ${A} - sed -i '/#include/ s///' "${S}/main.cpp" || die - sed -i -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm/' \ - -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ - -e 's/CFLGS=/CFLGS= ${CFLAGS} /' "${S}/makefile" || die -} - -src_compile() { - emake || die - emake -C misc/mktrace || die - emake -C misc/phd2fasta || die - (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die -} - -src_install() { - dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die - dobin scripts/* || die - insinto /usr/share/${PN}/examples - doins -r standard polyphred autofinish assembly_view 454_newbler align454reads align454reads_answer solexa_example solexa_example_answer selectRegions selectRegionsAnswer || die - echo 'CONSED_HOME=/usr' > "${S}/99consed" - doenvd "${S}/99consed" || die - dodoc README.txt *_announcement.txt -} -- cgit v1.2.3-65-gdbad