commit: 6d310e83f00757cb9568b49710d8f4eb93ee3840 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Mar 23 15:47:27 2014 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Mar 23 15:47:27 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6d310e83
sci-biology/consed: added versions 21 to 27 Package-Manager: portage-2.2.7 --- sci-biology/consed/ChangeLog | 21 ++++++++++- sci-biology/consed/consed-21.ebuild | 74 +++++++++++++++++++++++++++++++++++++ sci-biology/consed/consed-22.ebuild | 74 +++++++++++++++++++++++++++++++++++++ sci-biology/consed/consed-23.ebuild | 74 +++++++++++++++++++++++++++++++++++++ sci-biology/consed/consed-24.ebuild | 74 +++++++++++++++++++++++++++++++++++++ sci-biology/consed/consed-25.ebuild | 74 +++++++++++++++++++++++++++++++++++++ sci-biology/consed/consed-26.ebuild | 74 +++++++++++++++++++++++++++++++++++++ sci-biology/consed/consed-27.ebuild | 74 +++++++++++++++++++++++++++++++++++++ 8 files changed, 537 insertions(+), 2 deletions(-) diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog index 9221d45..3ce8ee3 100644 --- a/sci-biology/consed/ChangeLog +++ b/sci-biology/consed/ChangeLog @@ -1,8 +1,25 @@ # ChangeLog for sci-biology/consed -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*consed-27 (23 Mar 2014) +*consed-26 (23 Mar 2014) +*consed-25 (23 Mar 2014) +*consed-24 (23 Mar 2014) +*consed-23 (23 Mar 2014) +*consed-22 (23 Mar 2014) +*consed-21 (23 Mar 2014) + + 23 Mar 2014; Martin Mokrejs <[email protected]> + consed-20-r1.ebuild, +consed-21.ebuild, +consed-22.ebuild, + files/nLine.h.patch, files/nextPhredPipeline.cpp.patch, metadata.xml: + Added versions 21, 22, 23, 24, 25, 26, 27. None of them need the two + patches anymore but all of them need samtools for BAM support. + Compiled with x86_64-pc-linux-gnu-4.3.6. + 31 Oct 2012; Martin Mokrejs <[email protected]> consed-20-r1.ebuild: - renamed dependency from openmotif to motif consed-20-r1.ebuild + renamed dependency from openmotif to motif consed-20-r1.ebuild, + added some extra patches files/nLine.h.patch, + files/nextPhredPipeline.cpp.patch diff --git a/sci-biology/consed/consed-21.ebuild b/sci-biology/consed/consed-21.ebuild new file mode 100644 index 0000000..7163d60 --- /dev/null +++ b/sci-biology/consed/consed-21.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +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 -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die +} + +src_compile() { + emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" + emake -C misc/mktrace || die + emake -C misc/phd2fasta || die + (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die +} + +src_install() { + dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" + dobin scripts/* contributions/* || die + insinto /usr/lib/screenLibs + doins misc/*.{fa*,seq} || die + insinto /usr/share/${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-22.ebuild b/sci-biology/consed/consed-22.ebuild new file mode 100644 index 0000000..7163d60 --- /dev/null +++ b/sci-biology/consed/consed-22.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +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 -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die +} + +src_compile() { + emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" + emake -C misc/mktrace || die + emake -C misc/phd2fasta || die + (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die +} + +src_install() { + dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" + dobin scripts/* contributions/* || die + insinto /usr/lib/screenLibs + doins misc/*.{fa*,seq} || die + insinto /usr/share/${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-23.ebuild b/sci-biology/consed/consed-23.ebuild new file mode 100644 index 0000000..7163d60 --- /dev/null +++ b/sci-biology/consed/consed-23.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +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 -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die +} + +src_compile() { + emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" + emake -C misc/mktrace || die + emake -C misc/phd2fasta || die + (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die +} + +src_install() { + dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" + dobin scripts/* contributions/* || die + insinto /usr/lib/screenLibs + doins misc/*.{fa*,seq} || die + insinto /usr/share/${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-24.ebuild b/sci-biology/consed/consed-24.ebuild new file mode 100644 index 0000000..7163d60 --- /dev/null +++ b/sci-biology/consed/consed-24.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +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 -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die +} + +src_compile() { + emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" + emake -C misc/mktrace || die + emake -C misc/phd2fasta || die + (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die +} + +src_install() { + dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" + dobin scripts/* contributions/* || die + insinto /usr/lib/screenLibs + doins misc/*.{fa*,seq} || die + insinto /usr/share/${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-25.ebuild b/sci-biology/consed/consed-25.ebuild new file mode 100644 index 0000000..7163d60 --- /dev/null +++ b/sci-biology/consed/consed-25.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +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 -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die +} + +src_compile() { + emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" + emake -C misc/mktrace || die + emake -C misc/phd2fasta || die + (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die +} + +src_install() { + dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" + dobin scripts/* contributions/* || die + insinto /usr/lib/screenLibs + doins misc/*.{fa*,seq} || die + insinto /usr/share/${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-26.ebuild b/sci-biology/consed/consed-26.ebuild new file mode 100644 index 0000000..7163d60 --- /dev/null +++ b/sci-biology/consed/consed-26.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +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 -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die +} + +src_compile() { + emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" + emake -C misc/mktrace || die + emake -C misc/phd2fasta || die + (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die +} + +src_install() { + dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" + dobin scripts/* contributions/* || die + insinto /usr/lib/screenLibs + doins misc/*.{fa*,seq} || die + insinto /usr/share/${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 new file mode 100644 index 0000000..7163d60 --- /dev/null +++ b/sci-biology/consed/consed-27.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +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 -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die +} + +src_compile() { + emake || die "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152" + emake -C misc/mktrace || die + emake -C misc/phd2fasta || die + (cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die +} + +src_install() { + dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152" + dobin scripts/* contributions/* || die + insinto /usr/lib/screenLibs + doins misc/*.{fa*,seq} || die + insinto /usr/share/${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"; +}
