commit: 405438b9ea1ae2f88e025718f2dc0e55740c1e7e Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Mon Oct 3 19:21:02 2016 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Mon Oct 3 20:21:16 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=405438b9
sci-biology/consed: Remove old ebuilds Package-Manager: portage-2.3.1 sci-biology/consed/Manifest | 4 -- sci-biology/consed/consed-19-r2.ebuild | 71 --------------------------- sci-biology/consed/consed-27.ebuild | 90 ---------------------------------- 3 files changed, 165 deletions(-) diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest index 6761fed..f1a492d 100644 --- a/sci-biology/consed/Manifest +++ b/sci-biology/consed/Manifest @@ -1,6 +1,2 @@ -DIST consed-19-linux.tar.gz 29835559 SHA256 27501d714e4cd7ea04def6a7f985b674bc454ed8bd7d1e86b41b0283e2b9e089 -DIST consed-19-sources.tar.gz 6867357 SHA256 1db37b17608e49470926dae261c76d400cf3f9eb5feea52cd732e0bfa4cadee3 -DIST consed-27-linux.tar.gz 1604 SHA256 d7baafcbcdbf1b25262578511da8a51758f48d97d9109b334978acd150461855 SHA512 dbafb8c8f40dbed82a0000314549452c372e447467ccd8ec1004f44946dd09fcffa065c36bcca4f3c0fd55a137e570c135f4f79820e3e6d98626f92413b2731b WHIRLPOOL ae319734572558dd0047dad085c9f907386be6f7f0041bac0df9e1ce5b7558c750d92ea747cc3e74c594c83bed4cd73f4b37b4d6b9e39fd7caa2a733d67d6e21 -DIST consed-27-sources.tar.gz 1604 SHA256 d7baafcbcdbf1b25262578511da8a51758f48d97d9109b334978acd150461855 SHA512 dbafb8c8f40dbed82a0000314549452c372e447467ccd8ec1004f44946dd09fcffa065c36bcca4f3c0fd55a137e570c135f4f79820e3e6d98626f92413b2731b WHIRLPOOL ae319734572558dd0047dad085c9f907386be6f7f0041bac0df9e1ce5b7558c750d92ea747cc3e74c594c83bed4cd73f4b37b4d6b9e39fd7caa2a733d67d6e21 DIST consed-29-linux.tar.gz 36172715 SHA256 98354e2507ef9026b82c89db199ff1de7e4ec3686fccd691d215acdcde34ce39 SHA512 63a95d84cb58009045a9d898c8b1a94f98516bed9189f624a5930338cc8f51562504257f309d945fafcc07e0811ffeea122b640789f75fbd6c94535178dab4dd WHIRLPOOL 26ebc1ee7114b0c609fd36c2c46b71c399bacb61f7db285ab36f296902964c14518c058e814a166b20a36c2d320280aeed0ca18b7104c6b503324bf27d4b57af DIST consed-29-sources.tar.gz 3258845 SHA256 e7d3c2bf60e0bb22025e0416d16cf9864fec8091811ec285a39db4cb46bc3fc6 SHA512 fd711a65a02ef1238cca12b90fe7fa9b67da6c37d43cd105f38c7b6475fbc073c1f4d7f99703dec9d3a0a7a2a9317cb14999a114bb6f52589cb9b6e34700eb93 WHIRLPOOL 5ac363f049b6b40554112f830e812e7ab7d334a0f6707ea4da981ed1e468109f3bd7669382aa77e93cf12c78cc95fb1085711dcc972c7ff22ffe6b73056bb2c2 diff --git a/sci-biology/consed/consed-19-r2.ebuild b/sci-biology/consed/consed-19-r2.ebuild deleted file mode 100644 index 3ce704e..00000000 --- a/sci-biology/consed/consed-19-r2.ebuild +++ /dev/null @@ -1,71 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=3 - -inherit toolchain-funcs - -DESCRIPTION="A genome sequence finishing program" -HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"; -SRC_URI="${P}-sources.tar.gz - ${P}-linux.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND=">=x11-libs/motif-2.3:0" -RDEPEND="${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 ${DISTDIR}" -} - -src_prepare() { - sed -i '/#include/ s/<new.h>/<new>/' "${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 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/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) ${CFLAGS} sff2scf.c -o sff2scf) || die -} - -src_install() { - dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die - dobin scripts/* contributions/* || die - insinto /usr/lib/screenLibs - doins misc/*.{fa*,seq} || die - insinto /usr/share/${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='${EPREFIX}'/usr' > "${S}/99consed" - doenvd "${S}/99consed" || die - dodoc README.txt *_announcement.txt || die -} - -pkg_postinst() { - einfo "Package documentation is available at" - einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"; -} diff --git a/sci-biology/consed/consed-27.ebuild b/sci-biology/consed/consed-27.ebuild deleted file mode 100644 index 0bf33a7..00000000 --- a/sci-biology/consed/consed-27.ebuild +++ /dev/null @@ -1,90 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="A genome sequence finishing program" -HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"; -SRC_URI=" - ${P}-sources.tar.gz - ${P}-linux.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND=">=x11-libs/motif-2.3:0" -RDEPEND="${DEPEND} - sci-biology/samtools - >=sci-biology/phred-000925 - >=sci-biology/phrap-1.080721 - dev-lang/perl" - -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 ${DISTDIR}" -} - -src_prepare() { - sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die - sed -i \ - -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ - -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ - -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ - -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${S}/makefile" || die - sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die - sed \ - -e 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' \ - -i "${S}"/scripts/* || die -} - -src_compile() { - emake - emake -C misc/mktrace - emake -C misc/phd2fasta - (cd misc/454; $(tc-getCC) ${CFLAGS} ${LDFLAGS} sff2scf.c -o sff2scf) || die -} - -src_install() { - dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} - dobin scripts/* contributions/* - insinto /usr/lib/screenLibs - doins misc/*.{fa*,seq} - insinto /usr/share/${PN}/examples - doins -r \ - standard polyphred autofinish assembly_view 454_newbler \ - align454reads align454reads_answer solexa_example \ - solexa_example_answer selectRegions selectRegionsAnswer - echo 'CONSED_HOME="${EPREFIX}/usr"' > "${S}"/99consed || die - echo 'CONSED_PARAMETERS="${EPREFIX}/etc/consedrc"' >> "${S}"/99consed || die - mkdir -p "${ED}"/etc/consedrc || die - touch "${ED}"/etc/consedrc || die - doenvd "${S}/99consed" || die - sed \ - -e "s#/usr/local/genome#${EPREFIX}/usr#" \ - -i "${ED}"/usr/bin/{*.perl,phredPhrap,phredPhrapWithPhdBalls} || die - sed \ - -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' \ - -i "${ED}"/usr/bin/phredPhrap || die - sed \ - -e 's#/wt1/gordon/genome#/usr/bin#' \ - -i "${ED}"/usr/bin/fastq2Phrap.perl || die - dodoc README.txt *_announcement.txt || die -} - -pkg_postinst() { - einfo "Package documentation is available at" - einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"; -}
