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author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
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committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/consed/consed-29.ebuild |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/consed/consed-29.ebuild')
-rw-r--r-- | sci-biology/consed/consed-29.ebuild | 110 |
1 files changed, 110 insertions, 0 deletions
diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild new file mode 100644 index 000000000000..d5417e310281 --- /dev/null +++ b/sci-biology/consed/consed-29.ebuild @@ -0,0 +1,110 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic 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="examples" + +COMMON_DEPEND=" + x11-libs/libX11 + x11-libs/motif:0 + sci-biology/samtools:0.1-legacy +" +DEPEND=" + ${COMMON_DEPEND} + virtual/pkgconfig +" +RDEPEND=" + ${COMMON_DEPEND} + dev-lang/perl + >=sci-biology/phred-071220-r1 + >=sci-biology/phrap-1.080812-r2 +" + +S="${WORKDIR}" + +RESTRICT="fetch" +PATCHES=( + "${FILESDIR}/${PN}-29-fix-build-system.patch" + "${FILESDIR}/${PN}-29-fix-c++14.patch" + "${FILESDIR}/${PN}-29-fix-qa.patch" + "${FILESDIR}/${PN}-29-fix-perl-shebang.patch" +) + +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 ${DISTDIR}" +} + +src_prepare() { + default + + sed \ + -e "s!\$szPhredParameterFile = .*!\$szPhredParameterFile = \$ENV{'PHRED_PARAMETER_FILE'} || \'"${EPREFIX}"/usr/share/phred/phredpar.dat\';!" \ + -e "s:/usr/local/genome:${EPREFIX}/usr:" \ + -e "s:niceExe = \"/bin/nice\":niceExe = \"${EPREFIX}/usr/bin/nice\":" \ + -e "s:/wt1/gordon/genome:${EPREFIX}/usr/bin:" \ + -i scripts/* contributions/* || die +} + +src_configure() { + append-cflags -std=gnu99 + append-lfs-flags +} + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CXX="$(tc-getCXX)" \ + CFLAGS="${CFLAGS}" \ + CXXFLAGS="${CXXFLAGS}" \ + CPPFLAGS="${CPPFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + SAMTOOLS_CPPFLAGS="-I${EPREFIX}/usr/include/bam-0.1-legacy" \ + LIBS="-L${EPREFIX}/usr/$(get_libdir)" \ + X11_LIBS="$($(tc-getPKG_CONFIG) --libs x11)" \ + SAMTOOLS_LIBS="-lbam-0.1-legacy" +} + +src_install() { + dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} scripts/* contributions/* + + insinto /usr/lib/screenLibs + doins misc/*.{fa*,seq} + + if use examples; then + insinto /usr/share/${PN}/examples + doins -r \ + standard polyphred autofinish assembly_view 454_newbler \ + align454reads align454reads_answer solexa_example \ + solexa_example_answer selectRegions selectRegionsAnswer + fi + + cat > 99consed <<-_EOF_ || die + CONSED_HOME=${EPREFIX}/usr + CONSED_PARAMETERS=${EPREFIX}/etc/consedrc + _EOF_ + doenvd 99consed + + dodoc README.txt *_announcement.txt +} + +pkg_postinst() { + einfo "Package documentation is available at" + einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt" +} |