sci-biology/SEECER: patch crappy shellscripts to at leats die on error; require jellyfish-1.1.11

Package-Manager: portage-2.2.18

3 files changed, 48 insertions, 7 deletions

diff --git a/sci-biology/SEECER/ChangeLog b/sci-biology/SEECER/ChangeLog
index 2872b27ef..b72cc461e 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 <mmokrejs@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 <mmokrejs@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 730c4291e..3a9138c04 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 9258e5005..4e317e6b0 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;