[gentoo-commits] proj/sci:master commit in: sci-biology/consed/

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

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"