From c10c56b06fbaf0b0127db70aa6ad7b7910694d2e Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Fri, 13 Nov 2015 18:26:00 +0100 Subject: sci-biology/SEECER: remove hardcoded paths Package-Manager: portage-2.2.18 --- sci-biology/SEECER/ChangeLog | 7 ++++ sci-biology/SEECER/SEECER-0.1.3-r1.ebuild | 35 ---------------- sci-biology/SEECER/SEECER-0.1.3-r2.ebuild | 38 +++++++++++++++++ .../SEECER/files/remove-hardcoded-paths.patch | 49 ++++++++++++++++++++++ 4 files changed, 94 insertions(+), 35 deletions(-) delete mode 100644 sci-biology/SEECER/SEECER-0.1.3-r1.ebuild create mode 100644 sci-biology/SEECER/SEECER-0.1.3-r2.ebuild create mode 100644 sci-biology/SEECER/files/remove-hardcoded-paths.patch (limited to 'sci-biology/SEECER') diff --git a/sci-biology/SEECER/ChangeLog b/sci-biology/SEECER/ChangeLog index eae131d7c..2872b27ef 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 + +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 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-r1.ebuild deleted file mode 100644 index 1110b97e0..000000000 --- a/sci-biology/SEECER/SEECER-0.1.3-r1.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -DESCRIPTION="SEquencing Error Corrector for RNA-Seq reads" -HOMEPAGE="http://sb.cs.cmu.edu/seecer/" -SRC_URI=" - http://sb.cs.cmu.edu/seecer/downloads/"${P}".tar.gz - http://sb.cs.cmu.edu/seecer/downloads/manual.pdf -> "${PN}"-manual.pdf" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" -IUSE="" - -# although has bundled jellyfish-1.1.11 copy it just calls the executable during runtime -DEPEND=" - sci-libs/gsl - sci-biology/seqan" -RDEPEND="${DEPEND} - sci-biology/jellyfish" - -S="${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 -} - -src_install(){ - dobin bin/seecer bin/random_sub_N bin/replace_ids bin/run_jellyfish.sh bin/run_seecer.sh - dodoc README "${DISTDIR}"/"${PN}"-manual.pdf -} diff --git a/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild new file mode 100644 index 000000000..730c4291e --- /dev/null +++ b/sci-biology/SEECER/SEECER-0.1.3-r2.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils + +DESCRIPTION="SEquencing Error Corrector for RNA-Seq reads" +HOMEPAGE="http://sb.cs.cmu.edu/seecer/" +SRC_URI=" + http://sb.cs.cmu.edu/seecer/downloads/"${P}".tar.gz + http://sb.cs.cmu.edu/seecer/downloads/manual.pdf -> "${PN}"-manual.pdf" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +# although has bundled jellyfish-1.1.11 copy it just calls the executable during runtime +DEPEND=" + sci-libs/gsl + sci-biology/seqan" +RDEPEND="${DEPEND} + sci-biology/jellyfish" + +S="${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 "${FILESDIR}"/remove-hardcoded-paths.patch +} + +src_install(){ + dobin bin/seecer bin/random_sub_N bin/replace_ids bin/run_jellyfish.sh bin/run_seecer.sh + dodoc README "${DISTDIR}"/"${PN}"-manual.pdf +} 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 000000000..9258e5005 --- /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; + -- cgit v1.2.3-65-gdbad