# HG changeset patch # User jjohnson # Date 1508360157 14400 # Node ID aedaa66483f1cb80f97f2a9e41f121855b265c93 # Parent 225750bf37704bab156909c705d22cced65c4e17 Uploaded diff -r 225750bf3770 -r aedaa66483f1 config_sub.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config_sub.sh Wed Oct 18 16:55:57 2017 -0400 @@ -0,0 +1,27 @@ +#!/bin/bash +## substitute pathnames into config file +#!/bin/bash +SAMTOOLS_BIN=`which samtools` +BOWTIE_BIN=`which bowtie` +BOWTIE_BUILD_BIN=`which bowtie-build` +BLAT_BIN=`which blat` +FATOTWOBIT_BIN=`which faToTwoBit` +GMAP_BIN=`which gmap` +GMAP_BUILD_BIN=`which gmap_build` +GMAP_SETUP_BIN=$GMAP_BUILD_BIN +R_BIN=`which R` +RSCRIPT_BIN=`which Rscript` + +cat $1 | sed "s#__SAMTOOLS_BIN__#${SAMTOOLS_BIN}#"| \ +sed "s#__BOWTIE_BIN__#${BOWTIE_BIN}#"| \ +sed "s#__BOWTIE_BUILD_BIN__#${BOWTIE_BUILD_BIN}#" | \ +sed "s#__BLAT_BIN__#${BLAT_BIN}#"| \ +sed "s#__FATOTWOBIT_BIN__#${FATOTWOBIT_BIN}#" | \ +sed "s#__GMAP_BIN__#${GMAP_BIN}#" | \ +sed "s#^gmap_setup_bin#gmap_build_bin#" | \ +sed "s#__GMAP_SETUP_BIN__#${GMAP_SETUP_BIN}#" | \ +sed "s#__GMAP_BUILD_BIN__#${GMAP_BUILD_BIN}#" | \ +sed "s#__R_BIN__#${R_BIN}#" | \ +sed "s#__RSCRIPT_BIN__#${RSCRIPT_BIN}#" > $2 + +## if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi diff -r 225750bf3770 -r aedaa66483f1 create_reference_dataset.xml --- a/create_reference_dataset.xml Mon Jan 04 15:55:00 2016 -0500 +++ b/create_reference_dataset.xml Wed Oct 18 16:55:57 2017 -0400 @@ -5,7 +5,6 @@ - /bin/bash $defuse_script diff -r 225750bf3770 -r aedaa66483f1 datamanager_create_reference.xml --- a/datamanager_create_reference.xml Mon Jan 04 15:55:00 2016 -0500 +++ b/datamanager_create_reference.xml Wed Oct 18 16:55:57 2017 -0400 @@ -1,19 +1,19 @@ - + create a defuse reference from Ensembl and UCSC sources - - defuse - samtools - bowtie - gmap - kent - - datamanager_create_reference.py - --dbkey $genome.ensembl_genome_version - --description "$genome.ensembl_prefix $genome.ensembl_genome_version ($genome.ucsc_genome_version)" - --defuse_config $defuse_config - --defuse_script $defuse_script - $out_file - + + macros.xml + + + + + @@ -191,6 +191,7 @@ fatotwobit_bin = __FATOTWOBIT_BIN__ gmap_bin = __GMAP_BIN__ gmap_setup_bin = __GMAP_SETUP_BIN__ +gmap_build_bin = __GMAP_BUILD_BIN__ r_bin = __R_BIN__ rscript_bin = __RSCRIPT_BIN__ @@ -246,29 +247,29 @@ remove_job_temp_files = yes #end raw - #slurp + /dev/null`;then sed -i'.tmp' "s#__DATASET_DIRECTORY__#\$DATASET_DIRECTORY#" $defuse_config; fi +if `grep __DEFUSE_PATH__ $defuse_config > /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi +if `grep __SAMTOOLS_BIN__ $defuse_config > /dev/null` && SAMTOOLS_BIN=`which samtools`;then sed -i'.tmp' "s#__SAMTOOLS_BIN__#\${SAMTOOLS_BIN}#" $defuse_config; fi +if `grep __BOWTIE_BIN__ $defuse_config > /dev/null` && BOWTIE_BIN=`which bowtie`;then sed -i'.tmp' "s#__BOWTIE_BIN__#\${BOWTIE_BIN}#" $defuse_config; fi +if `grep __BOWTIE_BUILD_BIN__ $defuse_config > /dev/null` && BOWTIE_BUILD_BIN=`which bowtie-build`;then sed -i'.tmp' "s#__BOWTIE_BUILD_BIN__#\${BOWTIE_BUILD_BIN}#" $defuse_config; fi +if `grep __BLAT_BIN__ $defuse_config > /dev/null` && BLAT_BIN=`which blat`;then sed -i'.tmp' "s#__BLAT_BIN__#\${BLAT_BIN}#" $defuse_config; fi +if `grep __FATOTWOBIT_BIN__ $defuse_config > /dev/null` && FATOTWOBIT_BIN=`which faToTwoBit`;then sed -i'.tmp' "s#__FATOTWOBIT_BIN__#\${FATOTWOBIT_BIN}#" $defuse_config; fi +if `grep __GMAP_BIN__ $defuse_config > /dev/null` && GMAP_BIN=`which gmap`;then sed -i'.tmp' "s#__GMAP_BIN__#\${GMAP_BIN}#" $defuse_config; fi +if `grep __GMAP_BUILD_BIN__ $defuse_config > /dev/null` && GMAP_BUILD_BIN=`which gmap_setup`;then sed -i'.tmp' "s#__GMAP_BUILD_BIN__#\${GMAP_BUILD_BIN}#" $defuse_config; fi +if `grep __GMAP_INDEX_DIR__ $defuse_config > /dev/null` && GMAP_INDEX_DIR=`pwd`/gmap;then sed -i'.tmp' "s#__GMAP_INDEX_DIR__#\${GMAP_INDEX_DIR}#" $defuse_config; fi +if `grep __R_BIN__ $defuse_config > /dev/null` && R_BIN=`which R`;then sed -i'.tmp' "s#__R_BIN__#\${R_BIN}#" $defuse_config; fi +if `grep __RSCRIPT_BIN__ $defuse_config > /dev/null` && RSCRIPT_BIN=`which Rscript`;then sed -i'.tmp' "s#__RSCRIPT_BIN__#\${RSCRIPT_BIN}#" $defuse_config; fi ## copy config to output cp $defuse_config \$1/defuse_config.txt -## Run the create_reference_dataset.pl -perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config - +## Run defuse_create_ref.pl +defuse_create_ref.pl --config $defuse_config --dataset $DATASET_DIRECTORY + ]]> diff -r 225750bf3770 -r aedaa66483f1 defuse.xml --- a/defuse.xml Mon Jan 04 15:55:00 2016 -0500 +++ b/defuse.xml Wed Oct 18 16:55:57 2017 -0400 @@ -5,10 +5,33 @@ - - - /bin/bash $shscript + cluster_id_list && + get_fusion_fastq.pl --list cluster_id_list --output output_dir --fastq1 results.fusions_1.fq --fastq2 results.fusions_2.fq && + cp output_dir/results.* . && + cp `find output_dir -name defuse.log` $defuse_log + #if $defuse_out.__str__ != 'None': + && $__tool_directory__/make_html.sh $defuse_out $defuse_out.dataset.extra_files_path + #end if + ]]> @@ -61,10 +84,18 @@ + + + + Position density when calculating covariance + + Maximum number of alignments for a read pair, Pairs with more alignments are filtered, default is 10 + + @@ -76,29 +107,22 @@ - + - - - keep_output == True - - - - do_get_reads == True - - - breakpoints_bam == True - + + + +