commit: c10c56b06fbaf0b0127db70aa6ad7b7910694d2e Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Nov 13 17:26:00 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Nov 13 17:26:00 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c10c56b0
sci-biology/SEECER: remove hardcoded paths Package-Manager: portage-2.2.18 sci-biology/SEECER/ChangeLog | 7 ++++ ...ECER-0.1.3-r1.ebuild => SEECER-0.1.3-r2.ebuild} | 3 ++ .../SEECER/files/remove-hardcoded-paths.patch | 49 ++++++++++++++++++++++ 3 files changed, 59 insertions(+) diff --git a/sci-biology/SEECER/ChangeLog b/sci-biology/SEECER/ChangeLog index eae131d..2872b27 100644 --- a/sci-biology/SEECER/ChangeLog +++ b/sci-biology/SEECER/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Id$ +*SEECER-0.1.3-r2 (13 Nov 2015) + + 13 Nov 2015; Martin Mokrejs <[email protected]> + +SEECER-0.1.3-r2.ebuild, +files/remove-hardcoded-paths.patch, + -SEECER-0.1.3-r1.ebuild: + sci-biology/SEECER: remove hardcoded paths + 12 Nov 2015; Martin Mokrejs <[email protected]> SEECER-0.1.3-r1.ebuild: sci-biology/SEECER: install also the main program wrapper diff --git a/sci-biology/SEECER/SEECER-0.1.3-r1.ebuild b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild similarity index 93% rename from sci-biology/SEECER/SEECER-0.1.3-r1.ebuild rename to sci-biology/SEECER/SEECER-0.1.3-r2.ebuild index 1110b97..730c429 100644 --- a/sci-biology/SEECER/SEECER-0.1.3-r1.ebuild +++ b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild @@ -4,6 +4,8 @@ EAPI=5 +inherit eutils + DESCRIPTION="SEquencing Error Corrector for RNA-Seq reads" HOMEPAGE="http://sb.cs.cmu.edu/seecer/"; SRC_URI=" @@ -27,6 +29,7 @@ S="${S}"/SEECER src_prepare(){ # http://seecer-rna-read-error-correction-mailing-list.21961.x6.nabble.com/Segmentation-fault-in-step-4-td41.html cp -p "${FILESDIR}"/replace_ids.cc "${S}"/src/ || die + epatch "${FILESDIR}"/remove-hardcoded-paths.patch } src_install(){ diff --git a/sci-biology/SEECER/files/remove-hardcoded-paths.patch b/sci-biology/SEECER/files/remove-hardcoded-paths.patch new file mode 100644 index 0000000..9258e50 --- /dev/null +++ b/sci-biology/SEECER/files/remove-hardcoded-paths.patch @@ -0,0 +1,49 @@ +--- 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 +@@ -25,8 +25,8 @@ + # + + +-BINDIR='bin/' #this can be hardcoded to /absolute/path/to/SEECER/bin/ +-JF="../jellyfish-1.1.11/bin/jellyfish" #this may be hardcoded to /absolute/path/to/jellyfish/bin/ ++BINDIR='' #this can be hardcoded to /absolute/path/to/SEECER/bin/ ++JF="jellyfish" #this may be hardcoded to /absolute/path/to/jellyfish/bin/ + + K=17 + SEECER_PARAMS="" +@@ -149,7 +149,7 @@ + then + echo "++ Step 1: Replacing Ns ... and stripping off read IDs" + echo +- ${BINDIR}/random_sub_N $RS_ARGS ++ "${BINDIR}"random_sub_N $RS_ARGS + fi; + + if [ ! -r $Read1_N ]; +@@ -166,7 +166,7 @@ + then + 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 + fi; + + if [ ! -r $TMPDIR/counts_${K}_${LCOUNT} ]; +@@ -185,7 +185,7 @@ + echo "-----------------------------------------------------------------------" + 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 + echo " *** End time: " `date`; + echo "-----------------------------------------------------------------------" + echo +@@ -204,7 +204,7 @@ + if [ $SeecerStep -le 4 ]; + 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 + # rm $TMPDIR/corrected.fasta + fi; +
