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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2016-03-18 17:33:18 +0100 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2016-03-18 17:33:18 +0100 |
| commit | 2cf8dc31a6d127404c269bcd56d5e3ae96f823e2 (patch) | |
| tree | bb06de3c2c9d9d45d27ba9ec17a331d326421a86 /sci-biology | |
| parent | sci-biology/scythe: improve DESCRIPTION (diff) | |
| download | sci-2cf8dc31a6d127404c269bcd56d5e3ae96f823e2.tar.gz sci-2cf8dc31a6d127404c269bcd56d5e3ae96f823e2.tar.bz2 sci-2cf8dc31a6d127404c269bcd56d5e3ae96f823e2.zip | |
sci-biology/consed: fix the autogenerated /etc/env.d/ file and make sure the EPREFIX is expanded in it (should be also fixed in consed-27 in the main gentoo repo), check yourself 'printenv | grep CONSED' and do not forger env-update && . /etc/profile before re-testing; the first part of the patch now properly edits the variable in perl-based scripts/*; however, I am still getting some issue with 'consed -ace 454Contigs.ace.1 -fixContigEnds' giving me:\nabout to run: /usr/bin/fixContigEnd.perl right_contig00004|m.2.ref_160318.171619.fasta right_contig00004|m.2.ref_160318.171619.fixConsensusEndAceFile.fof\nUse of uninitialized value [1] in string eq at /usr/bin/fixContigEnd.perl line 21.\nsh: m.2.ref_160318.171619.fasta: command not found\nsh: m.2.ref_160318.171619.fixConsensusEndAceFile.fof: command not found\n
Package-Manager: portage-2.2.26
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/consed/consed-29.ebuild | 8 |
1 files changed, 4 insertions, 4 deletions
diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild index 46144771b..0a8387c0d 100644 --- a/sci-biology/consed/consed-29.ebuild +++ b/sci-biology/consed/consed-29.ebuild @@ -48,12 +48,12 @@ 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 @@ -70,8 +70,8 @@ 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 + 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" |