# 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
-
+
+
+
+