# HG changeset patch
# User jjohnson
# Date 1508421954 14400
# Node ID e500b50b72fd59937e1c23ce52257d4ac753d485
# Parent aedaa66483f1cb80f97f2a9e41f121855b265c93
Uploaded
diff -r aedaa66483f1 -r e500b50b72fd config_sub.sh
--- a/config_sub.sh Wed Oct 18 16:55:57 2017 -0400
+++ b/config_sub.sh Thu Oct 19 10:05:54 2017 -0400
@@ -11,9 +11,11 @@
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__#${BOWTIE_BIN}#"| \
+DEFUSE_BIN=`which defuse_run.pl`
+DEFUSE_PATH=`python -c "import os.path; print os.path.dirname(os.path.dirname(os.path.realpath(\"$DEFUSE_BIN\")))"`
+cat $1 | sed "s#__DEFUSE_PATH__#${DEFUSE_PATH}#" | \
+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__#${FATOTWOBIT_BIN}#" | \
@@ -23,5 +25,5 @@
sed "s#__GMAP_BUILD_BIN__#${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
+export DATASET_DIRECTORY=`grep '^dataset_directory' $1 | awk '{print \$NF}'`
+echo "$DATASET_DIRECTORY"
diff -r aedaa66483f1 -r e500b50b72fd defuse.xml
--- a/defuse.xml Wed Oct 18 16:55:57 2017 -0400
+++ b/defuse.xml Thu Oct 19 10:05:54 2017 -0400
@@ -9,27 +9,28 @@
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
+ cp `find -L 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
+ && $__tool_directory__/make_html.sh $defuse_out $defuse_out.files_path
#end if
]]>
@@ -110,8 +111,6 @@
-
-
diff -r aedaa66483f1 -r e500b50b72fd make_html.sh