commit: 6af16cbc76de1d4d8a1726e81880cfccb28adbb6
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Nov 13 19:03:02 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Nov 13 19:03:02 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6af16cbc
sci-biology/SEECER: patch crappy shellscripts to at leats die on error; require
jellyfish-1.1.11
Package-Manager: portage-2.2.18
sci-biology/SEECER/ChangeLog | 5 +++
sci-biology/SEECER/SEECER-0.1.3-r2.ebuild | 3 +-
.../SEECER/files/remove-hardcoded-paths.patch | 47 +++++++++++++++++++---
3 files changed, 48 insertions(+), 7 deletions(-)
diff --git a/sci-biology/SEECER/ChangeLog b/sci-biology/SEECER/ChangeLog
index 2872b27..b72cc46 100644
--- a/sci-biology/SEECER/ChangeLog
+++ b/sci-biology/SEECER/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 13 Nov 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz>
+ SEECER-0.1.3-r2.ebuild, files/remove-hardcoded-paths.patch:
+ sci-biology/SEECER: patch crappy shellscripts to at leats die on error;
+ require jellyfish-1.1.11
+
*SEECER-0.1.3-r2 (13 Nov 2015)
13 Nov 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz>
diff --git a/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
index 730c429..3a9138c 100644
--- a/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
+++ b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild
@@ -18,11 +18,12 @@ KEYWORDS="~amd64"
IUSE=""
# although has bundled jellyfish-1.1.11 copy it just calls the executable
during runtime
+# seems jellyfish-2 does not accept same commandline arguments
DEPEND="
sci-libs/gsl
sci-biology/seqan"
RDEPEND="${DEPEND}
- sci-biology/jellyfish"
+ =sci-biology/jellyfish-1.1.11"
S="${S}"/SEECER
diff --git a/sci-biology/SEECER/files/remove-hardcoded-paths.patch
b/sci-biology/SEECER/files/remove-hardcoded-paths.patch
index 9258e50..4e317e6 100644
--- a/sci-biology/SEECER/files/remove-hardcoded-paths.patch
+++ b/sci-biology/SEECER/files/remove-hardcoded-paths.patch
@@ -1,5 +1,40 @@
---- SEECER-0.1.3/SEECER/bin/run_seecer.sh.old 2015-11-13 18:17:53.985784977
+0100
-+++ SEECER-0.1.3/SEECER/bin/run_seecer.sh 2015-11-13 18:20:19.995787411
+0100
+--- SEECER-0.1.3/SEECER/bin/run_jellyfish.sh.ori 2015-11-13
18:40:01.595807104 +0100
++++ SEECER-0.1.3/SEECER/bin/run_jellyfish.sh 2015-11-13 18:51:45.655818838
+0100
+@@ -3,22 +3,27 @@
+ LCOUNT=$4
+ TMPDIR=$5
+
++if [ -z "$JF" ]; then
++ echo "No path to jellyfish binary provided, exiting.";
++ exit 255;
++fi
++
+ if [ "$#" -eq "4" ];
+ then
+-$JF count -m $3 -o $TMPDIR/jf_tmp -c 3 -s 10000000 -t 32 --both-strands $6
++$JF count -m $3 -o $TMPDIR/jf_tmp -c 3 -s 10000000 -t 32 --both-strands $6 ||
exit 255
+ else
+-$JF count -m $3 -o $TMPDIR/jf_tmp -c 3 -s 10000000 -t 32 --both-strands $6 $7
++$JF count -m $3 -o $TMPDIR/jf_tmp -c 3 -s 10000000 -t 32 --both-strands $6 $7
|| exit 255
+ fi;
+
+ # merge
+ N_TMP=`ls -1 $TMPDIR/jf_tmp_* | wc -l`
+ if [ $N_TMP -eq 1 ]
+ then
+- mv $TMPDIR/jf_tmp_0 $TMPDIR/jf_merged_$3
++ mv $TMPDIR/jf_tmp_0 $TMPDIR/jf_merged_$3 || exit 255
+ else
+- $JF merge $TMPDIR/jf_tmp_* -o $TMPDIR/jf_merged_$3
++ $JF merge $TMPDIR/jf_tmp_* -o $TMPDIR/jf_merged_$3 || exit 255
+ rm $TMPDIR/jf_tmp_*
+ fi
+
+-$JF dump --lower-count=$LCOUNT -o $2 -c $TMPDIR/jf_merged_$3
++$JF dump --lower-count=$LCOUNT -o $2 -c $TMPDIR/jf_merged_$3 || exit 255
+ rm $TMPDIR/jf_merged_$3
+--- SEECER-0.1.3/SEECER/bin/run_seecer.sh.ori 2015-11-13 18:40:16.215807347
+0100
++++ SEECER-0.1.3/SEECER/bin/run_seecer.sh 2015-11-13 18:53:03.695820138
+0100
@@ -25,8 +25,8 @@
#
@@ -16,7 +51,7 @@
echo "++ Step 1: Replacing Ns ... and stripping off read IDs"
echo
- ${BINDIR}/random_sub_N $RS_ARGS
-+ "${BINDIR}"random_sub_N $RS_ARGS
++ "${BINDIR}"random_sub_N $RS_ARGS || exit 255
fi;
if [ ! -r $Read1_N ];
@@ -25,7 +60,7 @@
echo "++ Step 2: Running JELLYFISH to count kmers ..."
echo
- bash ${BINDIR}/run_jellyfish.sh $JF $TMPDIR/counts_${K}_${LCOUNT} $K
$LCOUNT $TMPDIR $Read1_N $Read2_N
-+ bash "${BINDIR}"run_jellyfish.sh $JF $TMPDIR/counts_${K}_${LCOUNT} $K
$LCOUNT $TMPDIR $Read1_N $Read2_N
++ bash "${BINDIR}"run_jellyfish.sh $JF $TMPDIR/counts_${K}_${LCOUNT} $K
$LCOUNT $TMPDIR $Read1_N $Read2_N || exit 255
fi;
if [ ! -r $TMPDIR/counts_${K}_${LCOUNT} ];
@@ -34,7 +69,7 @@
echo " *** Start time: " `date`;
- ${BINDIR}/seecer $Read1_N $Read2_N $SEECER_PARAMS --kmer $K -k
$TMPDIR/counts_${K}_${LCOUNT} -o $TMPDIR/corrected.fasta
-+ "${BINDIR}"seecer $Read1_N $Read2_N $SEECER_PARAMS --kmer $K -k
$TMPDIR/counts_${K}_${LCOUNT} -o $TMPDIR/corrected.fasta
++ "${BINDIR}"seecer $Read1_N $Read2_N $SEECER_PARAMS --kmer $K -k
$TMPDIR/counts_${K}_${LCOUNT} -o $TMPDIR/corrected.fasta || exit 255
echo " *** End time: " `date`;
echo
"-----------------------------------------------------------------------"
echo
@@ -43,7 +78,7 @@
then
echo "++ Step 4: Cleaning and putting back original read IDs ... We
finish soon!"
- ${BINDIR}/replace_ids $TMPDIR/corrected.fasta $Reads $Reads_N $Reads_O
-+ "${BINDIR}"replace_ids $TMPDIR/corrected.fasta $Reads $Reads_N $Reads_O
++ "${BINDIR}"replace_ids $TMPDIR/corrected.fasta $Reads $Reads_N $Reads_O
|| exit 255
# rm $TMPDIR/corrected.fasta
fi;
