sci-biology/consed: Remove old ebuilds

Package-Manager: portage-2.3.1

diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest
index 6761fedbfeea22a861569c163108af32ad4e11e0..f1a492de74cc12602c0a34c7a86e77080b151e4c 100644 (file)
--- 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 (file)
index 3ce704e..0000000
--- 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 (file)
index 0bf33a7..0000000
--- 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"
-}