commit: 2cf8dc31a6d127404c269bcd56d5e3ae96f823e2
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 18 16:33:18 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 18 16:33:18 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2cf8dc31
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
sci-biology/consed/consed-29.ebuild | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-biology/consed/consed-29.ebuild
b/sci-biology/consed/consed-29.ebuild
index 4614477..0a8387c 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"
