annotate tool_dependencies.xml @ 3:c758125c56d8 draft

Update to KggSeq release 0.8 (23/Apr./2015)
author crs4
date Mon, 25 May 2015 18:01:25 -0400
parents e9758eee6697
children a13b8ff61c6c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d388273fb83f Uploaded
crs4
parents:
diff changeset
1 <?xml version="1.0"?>
d388273fb83f Uploaded
crs4
parents:
diff changeset
2 <tool_dependency>
3
c758125c56d8 Update to KggSeq release 0.8 (23/Apr./2015)
crs4
parents: 1
diff changeset
3 <package name="kggseq" version="0.8_20150423">
0
d388273fb83f Uploaded
crs4
parents:
diff changeset
4 <install version="1.0">
d388273fb83f Uploaded
crs4
parents:
diff changeset
5 <actions>
3
c758125c56d8 Update to KggSeq release 0.8 (23/Apr./2015)
crs4
parents: 1
diff changeset
6 <action type="download_by_url" target_filename="kggseq_archive-v0.8_20150423.tar.gz">https://github.com/crs4/kggseq_archive/archive/v0.8_20150423.tar.gz</action>
0
d388273fb83f Uploaded
crs4
parents:
diff changeset
7 <action type="shell_command">touch test.vcf</action>
1
e9758eee6697 Update to KggSeq v0.7_20150118
crs4
parents: 0
diff changeset
8 <action type="shell_command">java -jar kggseq.jar --no-lib-check --resource resources --buildver hg19 --db-filter 1kg201305,1kg201204,1kgafr201204,1kgeur201204,1kgamr201204,1kgasn201204,dbsnp135,dbsnp137,dbsnp138,dbsnp138nf,dbsnp141,ESP6500AA,ESP6500EA,exac --genome-annot --db-gene refgene,gencode,knowngene,ensembl --db-score dbnsfp --superdup-annot --cosmic-annot --vcf-file test.vcf</action>
e9758eee6697 Update to KggSeq v0.7_20150118
crs4
parents: 0
diff changeset
9 <action type="shell_command">java -Xmx4g -jar kggseq.jar --no-lib-check --no-qc --resource resources --buildver hg19 --o-flanking-seq 10 --vcf-file examples/rare.disease.hg19.vcf</action>
0
d388273fb83f Uploaded
crs4
parents:
diff changeset
10 <action type="move_directory_files">
d388273fb83f Uploaded
crs4
parents:
diff changeset
11 <source_directory>.</source_directory>
d388273fb83f Uploaded
crs4
parents:
diff changeset
12 <destination_directory>$INSTALL_DIR</destination_directory>
d388273fb83f Uploaded
crs4
parents:
diff changeset
13 </action>
d388273fb83f Uploaded
crs4
parents:
diff changeset
14 <action type="set_environment">
d388273fb83f Uploaded
crs4
parents:
diff changeset
15 <environment_variable name="KGGSEQ_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
d388273fb83f Uploaded
crs4
parents:
diff changeset
16 </action>
d388273fb83f Uploaded
crs4
parents:
diff changeset
17 </actions>
d388273fb83f Uploaded
crs4
parents:
diff changeset
18 </install>
d388273fb83f Uploaded
crs4
parents:
diff changeset
19 </package>
d388273fb83f Uploaded
crs4
parents:
diff changeset
20 </tool_dependency>