From 469d9c92643af1ef58cc1ca76ad3b70f41bc838f Mon Sep 17 00:00:00 2001 From: Sascha Steinbiss Date: Fri, 26 Jun 2015 11:15:39 +0100 Subject: [PATCH 1/2] use $baseDir consistently --- loc_sanger.config | 24 ++++++++++++------------ loc_sanger_farm.config | 24 ++++++++++++------------ loc_travis.config | 30 +++++++++++++++--------------- 3 files changed, 39 insertions(+), 39 deletions(-) diff --git a/loc_sanger.config b/loc_sanger.config index 773ddd4..5d0d3ce 100644 --- a/loc_sanger.config +++ b/loc_sanger.config @@ -1,21 +1,21 @@ env { - PATH = "${ROOTDIR}/RATT:${ROOTDIR}/ABACAS2:${HOME}/annot/software/ORTHOMCLV1.4:${HOME}/genometools/bin:/software/pathogen/external/apps/usr/local/tmhmm-2.0c/bin:${HOME}/annot/software/augustus-3.0.3/bin:/software/pathogen/external/apps/usr/bin:$PATH" - RATT_HOME = "${ROOTDIR}/RATT" - RATT_CONFIG = "${ROOTDIR}/RATT/RATT.config_euk_NoPseudo_SpliceSite" + PATH = "${baseDir}/RATT:${baseDir}/ABACAS2:${HOME}/annot/software/ORTHOMCLV1.4:${HOME}/genometools/bin:/software/pathogen/external/apps/usr/local/tmhmm-2.0c/bin:${HOME}/annot/software/augustus-3.0.3/bin:/software/pathogen/external/apps/usr/bin:$PATH" + RATT_HOME = "${baseDir}/RATT" + RATT_CONFIG = "${baseDir}/RATT/RATT.config_euk_NoPseudo_SpliceSite" GT_RETAINIDS = "yes" PFAM = "/lustre/scratch108/parasites/ss34/pfam/Pfam-A.hmm" - SNAP_MODEL = "${ROOTDIR}/data/snap/LmjF.hmm" - AUGUSTUS_CONFIG_PATH = "${ROOTDIR}/data/augustus" - FILTER_SHORT_PARTIALS_RULE = "${ROOTDIR}/data/filters/filter_short_partials.lua" - PFAM2GO = "${ROOTDIR}/data/pfam2go/pfam2go.txt" + SNAP_MODEL = "${baseDir}/data/snap/LmjF.hmm" + AUGUSTUS_CONFIG_PATH = "${baseDir}/data/augustus" + FILTER_SHORT_PARTIALS_RULE = "${baseDir}/data/filters/filter_short_partials.lua" + PFAM2GO = "${baseDir}/data/pfam2go/pfam2go.txt" } params.GO_OBO = "${HOME}/go.obo" -params.NCRNA_MODELS = "${ROOTDIR}/data/cm/kinetoplastid_rnas.cm" -params.CIRCOS_CONFIG_FILE = "${ROOTDIR}/data/circos/circos.conf" -params.CIRCOS_BIN_CONFIG_FILE = "${ROOTDIR}/data/circos/circos.bin.conf" -params.SPECFILE = "${ROOTDIR}/data/speck/new_gff_format.lua" -params.AUGUSTUS_EXTRINSIC_CFG = "${ROOTDIR}/data/augustus/extrinsic.cfg" +params.NCRNA_MODELS = "${baseDir}/data/cm/kinetoplastid_rnas.cm" +params.CIRCOS_CONFIG_FILE = "${baseDir}/data/circos/circos.conf" +params.CIRCOS_BIN_CONFIG_FILE = "${baseDir}/data/circos/circos.bin.conf" +params.SPECFILE = "${baseDir}/data/speck/new_gff_format.lua" +params.AUGUSTUS_EXTRINSIC_CFG = "${baseDir}/data/augustus/extrinsic.cfg" executor { name = 'local' diff --git a/loc_sanger_farm.config b/loc_sanger_farm.config index d074b2e..894b58a 100644 --- a/loc_sanger_farm.config +++ b/loc_sanger_farm.config @@ -1,21 +1,21 @@ env { - PATH = "${ROOTDIR}/RATT:${ROOTDIR}/ABACAS2:${HOME}/annot/software/ORTHOMCLV1.4:${HOME}/genometools/bin:/software/pathogen/external/apps/usr/local/tmhmm-2.0c/bin:${HOME}/annot/software/augustus-3.0.3/bin:/software/pathogen/external/apps/usr/bin:$PATH" - RATT_HOME = "${ROOTDIR}/RATT" - RATT_CONFIG = "${ROOTDIR}/RATT/RATT.config_euk_NoPseudo_SpliceSite" + PATH = "${baseDir}/RATT:${baseDir}/ABACAS2:${HOME}/annot/software/ORTHOMCLV1.4:${HOME}/genometools/bin:/software/pathogen/external/apps/usr/local/tmhmm-2.0c/bin:${HOME}/annot/software/augustus-3.0.3/bin:/software/pathogen/external/apps/usr/bin:$PATH" + RATT_HOME = "${baseDir}/RATT" + RATT_CONFIG = "${baseDir}/RATT/RATT.config_euk_NoPseudo_SpliceSite" GT_RETAINIDS = "yes" PFAM = "/lustre/scratch108/parasites/ss34/pfam/Pfam-A.hmm" - SNAP_MODEL = "${ROOTDIR}/data/snap/LmjF.hmm" - AUGUSTUS_CONFIG_PATH = "${ROOTDIR}/data/augustus" - FILTER_SHORT_PARTIALS_RULE = "${ROOTDIR}/data/filters/filter_short_partials.lua" - PFAM2GO = "${ROOTDIR}/data/pfam2go/pfam2go.txt" + SNAP_MODEL = "${baseDir}/data/snap/LmjF.hmm" + AUGUSTUS_CONFIG_PATH = "${baseDir}/data/augustus" + FILTER_SHORT_PARTIALS_RULE = "${baseDir}/data/filters/filter_short_partials.lua" + PFAM2GO = "${baseDir}/data/pfam2go/pfam2go.txt" } params.GO_OBO = "${HOME}/go.obo" -params.NCRNA_MODELS = "${ROOTDIR}/data/cm/kinetoplastid_rnas.cm" -params.CIRCOS_CONFIG_FILE = "${ROOTDIR}/data/circos/circos.conf" -params.CIRCOS_BIN_CONFIG_FILE = "${ROOTDIR}/data/circos/circos.bin.conf" -params.SPECFILE = "${ROOTDIR}/data/speck/new_gff_format.lua" -params.AUGUSTUS_EXTRINSIC_CFG = "${ROOTDIR}/data/augustus/extrinsic.cfg" +params.NCRNA_MODELS = "${baseDir}/data/cm/kinetoplastid_rnas.cm" +params.CIRCOS_CONFIG_FILE = "${baseDir}/data/circos/circos.conf" +params.CIRCOS_BIN_CONFIG_FILE = "${baseDir}/data/circos/circos.bin.conf" +params.SPECFILE = "${baseDir}/data/speck/new_gff_format.lua" +params.AUGUSTUS_EXTRINSIC_CFG = "${baseDir}/data/augustus/extrinsic.cfg" process.memory = "2 GB" process.clusterOptions = " -R 'select[mem>2048] rusage[mem=2048]' " diff --git a/loc_travis.config b/loc_travis.config index e2e91a8..768d669 100644 --- a/loc_travis.config +++ b/loc_travis.config @@ -1,22 +1,22 @@ env { - PATH = "${ROOTDIR}/RATT:${ROOTDIR}/ABACAS2:${ROOTDIR}/ORTHOMCLV1.4:${ROOTDIR}/genometools/bin:${ROOTDIR}/aragorn:${ROOTDIR}/augustus/bin:$PATH" - PERL5LIB = "${ROOTDIR}/ORTHOMCLV1.4/:${ROOTDIR}/RATT/:${ROOTDIR}/ABACAS2/:${PERL5LIB}" - RATT_HOME = "${ROOTDIR}/RATT" - RATT_CONFIG = "${ROOTDIR}/RATT/RATT.config_euk_NoPseudo_SpliceSite" + PATH = "${baseDir}/RATT:${baseDir}/ABACAS2:${baseDir}/ORTHOMCLV1.4:${baseDir}/genometools/bin:${baseDir}/aragorn:${baseDir}/augustus/bin:$PATH" + PERL5LIB = "${baseDir}/ORTHOMCLV1.4/:${baseDir}/RATT/:${baseDir}/ABACAS2/:${PERL5LIB}" + RATT_HOME = "${baseDir}/RATT" + RATT_CONFIG = "${baseDir}/RATT/RATT.config_euk_NoPseudo_SpliceSite" GT_RETAINIDS = "yes" - PFAM = "${ROOTDIR}/Pfam-A.hmm" - SNAP_MODEL = "${ROOTDIR}/data/snap/LmjF.hmm" - AUGUSTUS_CONFIG_PATH = "${ROOTDIR}/data/augustus" - FILTER_SHORT_PARTIALS_RULE = "${ROOTDIR}/data/filters/filter_short_partials.lua" - PFAM2GO = "${ROOTDIR}/data/pfam2go/pfam2go.txt" + PFAM = "${baseDir}/Pfam-A.hmm" + SNAP_MODEL = "${baseDir}/data/snap/LmjF.hmm" + AUGUSTUS_CONFIG_PATH = "${baseDir}/data/augustus" + FILTER_SHORT_PARTIALS_RULE = "${baseDir}/data/filters/filter_short_partials.lua" + PFAM2GO = "${baseDir}/data/pfam2go/pfam2go.txt" } -params.GO_OBO = "${ROOTDIR}/go.obo" -params.NCRNA_MODELS = "${ROOTDIR}/data/cm/kinetoplastid_rnas.cm" -params.CIRCOS_CONFIG_FILE = "${ROOTDIR}/data/circos/circos.debian.conf" -params.CIRCOS_BIN_CONFIG_FILE = "${ROOTDIR}/data/circos/circos.bin.debian.conf" -params.SPECFILE = "${ROOTDIR}/data/speck/new_gff_format.lua" -params.AUGUSTUS_EXTRINSIC_CFG = "${ROOTDIR}/data/augustus/extrinsic.cfg" +params.GO_OBO = "${baseDir}/go.obo" +params.NCRNA_MODELS = "${baseDir}/data/cm/kinetoplastid_rnas.cm" +params.CIRCOS_CONFIG_FILE = "${baseDir}/data/circos/circos.debian.conf" +params.CIRCOS_BIN_CONFIG_FILE = "${baseDir}/data/circos/circos.bin.debian.conf" +params.SPECFILE = "${baseDir}/data/speck/new_gff_format.lua" +params.AUGUSTUS_EXTRINSIC_CFG = "${baseDir}/data/augustus/extrinsic.cfg" executor { name = 'local' From 839d047d752650151e99ac09fe374a4322a3d2ce Mon Sep 17 00:00:00 2001 From: Sascha Steinbiss Date: Fri, 26 Jun 2015 11:15:57 +0100 Subject: [PATCH 2/2] whitespace --- nextflow.config | 3 --- 1 file changed, 3 deletions(-) diff --git a/nextflow.config b/nextflow.config index d09ad37..7d70ad5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -53,14 +53,11 @@ params { // output GAF metadata TAXON_ID = 4711 DB_ID = "GeneDB" - } profiles { - docker { includeConfig 'loc_docker.config' } sanger { includeConfig 'loc_sanger.config' } sanger_farm { includeConfig 'loc_sanger_farm.config' } travis { includeConfig 'loc_travis.config' } - } \ No newline at end of file