diff options
Diffstat (limited to 'sci-biology/consed/consed-29.ebuild')
| -rw-r--r-- | sci-biology/consed/consed-29.ebuild | 12 |
1 files changed, 6 insertions, 6 deletions
diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild index 46144771b..002e0074b 100644 --- a/sci-biology/consed/consed-29.ebuild +++ b/sci-biology/consed/consed-29.ebuild @@ -22,6 +22,7 @@ DEPEND=">=x11-libs/motif-2.3:0" # This file was about sci-biology/samtools-1.2 time moved to sci-libs/htslib-1.2.1 RDEPEND="${DEPEND} <sci-biology/samtools-1.0 + >=sci-biology/samtools-0.1.18 >=sci-biology/phred-000925 >=sci-biology/phrap-1.080721 dev-lang/perl" @@ -48,12 +49,12 @@ src_prepare() { -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/ -I/usr/include/htslib/#' "${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";!' \ + -e "s!\$szPhredParameterFile = .*!\$szPhredParameterFile = \$ENV{'PHRED_PARAMETER_FILE'} || \'"${EPREFIX}"/usr/share/phred/phredpar.dat\';!" \ -i "${S}"/scripts/* || die } src_compile() { - einfo "consed does not compile with sys-devel/gcc-4.6:* or newer (but 4.4.7 works)" + einfo "consed does not compile with >=sys-devel/gcc-4.6:* but 4.4.7 works" default emake -C misc/mktrace emake -C misc/phd2fasta @@ -70,10 +71,9 @@ src_install() { 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 + echo CONSED_HOME="${EPREFIX}"/usr > "${S}"/99consed || die + echo CONSED_PARAMETERS="${EPREFIX}"/etc/consedrc >> "${S}"/99consed || die + touch "${ED}"/etc/consedrc || die "Cannot create a file for system-wide settings" doenvd "${S}/99consed" sed \ -e "s#/usr/local/genome#${EPREFIX}/usr#" \ |