diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/consed/ChangeLog | 10 | ||||
| -rw-r--r-- | sci-biology/consed/consed-19-r1.ebuild | 71 | ||||
| -rw-r--r-- | sci-biology/consed/consed-27.ebuild | 90 |
3 files changed, 98 insertions, 73 deletions
diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog index 61c95626d70c..b6e3c6c1be36 100644 --- a/sci-biology/consed/ChangeLog +++ b/sci-biology/consed/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-biology/consed -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.7 2013/03/11 15:00:03 jlec Exp $ +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.8 2014/10/26 16:13:23 jlec Exp $ + +*consed-27 (26 Oct 2014) + + 26 Oct 2014; Justin Lecher <jlec@gentoo.org> -consed-19-r1.ebuild, + +consed-27.ebuild: + Import to tree; drop old EPAI=1 version, #526742 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: Drop Andrey as maintainer so that bugs get assigned to sci-biology directly diff --git a/sci-biology/consed/consed-19-r1.ebuild b/sci-biology/consed/consed-19-r1.ebuild deleted file mode 100644 index 18bd330c7e66..000000000000 --- a/sci-biology/consed/consed-19-r1.ebuild +++ /dev/null @@ -1,71 +0,0 @@ -# Copyright 1999-2012 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 1.4 2012/10/24 19:30:07 ulm Exp $ - -EAPI=1 - -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 - ${P}-linux.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="" - -DEPEND=">=x11-libs/motif-2.3:0" -RDEPEND="${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_unpack() { - unpack ${A} - sed -i '/#include/ s/<new.h>/<new>/' "${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 $ENV{PHRED_PARAMETER_FILE} || "/usr/share/phred/phredpar.dat";!' "${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' > "${S}/99consed" - doenvd "${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-27.ebuild b/sci-biology/consed/consed-27.ebuild new file mode 100644 index 000000000000..b56fccd7213b --- /dev/null +++ b/sci-biology/consed/consed-27.ebuild @@ -0,0 +1,90 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-27.ebuild,v 1.1 2014/10/26 16:13:23 jlec Exp $ + +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" +} |