# HG changeset patch
# User morinlab
# Date 1480893263 18000
# Node ID 679f610562de3ac71a0fa1ae6f80131960c770fb
Uploaded
diff -r 000000000000 -r 679f610562de manta/manta.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/manta/manta.xml Sun Dec 04 18:14:23 2016 -0500
@@ -0,0 +1,61 @@
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+ SV Caller
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+ manta
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+ ln -s $normal normal.bam;
+ ln -s $normal.metadata.bam_index normal.bam.bai;
+ ln -s $tumour tumour.bam;
+ ln -s $tumour.metadata.bam_index tumour.bam.bai;
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+
+ #if $reference_source.reference_source_selector == "history":
+ ln -s $reference_source.ref_file ref.fa;
+ samtools faidx ref.fa;
+ #end if
+
+ python \$MANTA_INSTALL_DIR/install/bin/configManta.py
+ --normalBam=normal.bam
+ --tumorBam=tumour.bam
+ #if $reference_source.reference_source_selector == "history":
+ --referenceFasta=ref.fa
+ #else
+ --referenceFasta=${reference_source.ref_file.fields.path}
+ #end if
+ --runDir=./output;
+
+ ./output/runWorkflow.py
+ -m local
+ -j \${GALAXY_SLOTS:-1}
+ --quiet;
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+ gunzip -c ./output/results/variants/somaticSV.vcf.gz > $output;
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diff -r 000000000000 -r 679f610562de manta/tool-data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/manta/tool-data/all_fasta.loc.sample Sun Dec 04 18:14:23 2016 -0500
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
diff -r 000000000000 -r 679f610562de manta/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/manta/tool_data_table_conf.xml.sample Sun Dec 04 18:14:23 2016 -0500
@@ -0,0 +1,6 @@
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+ value, dbkey, name, path
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diff -r 000000000000 -r 679f610562de manta/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/manta/tool_dependencies.xml Sun Dec 04 18:14:23 2016 -0500
@@ -0,0 +1,6 @@
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