Mercurial > repos > stef > falco
changeset 7:c84ed1b12d67 draft
Uploaded
author | stef |
---|---|
date | Thu, 11 Sep 2014 10:49:52 -0400 |
parents | cebbd6a92411 |
children | 44728b4dee38 |
files | falco.sh falco.xml tool_dependencies.xml |
diffstat | 3 files changed, 13 insertions(+), 0 deletions(-) [+] |
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--- a/falco.sh Thu Sep 11 06:59:12 2014 -0400 +++ b/falco.sh Thu Sep 11 10:49:52 2014 -0400 @@ -64,11 +64,20 @@ echo "HTMLOUT: "$html_out echo "VCFOUT : "$vcf_out echo "INIT : "$init_file + source $init_file + echo "--- sam ---" samtools echo "--- bcf ---" bcftools +echo "--- snpsift ---" +java -jar $snpSift/SnpSift.jar +echo "--- snpeff ---" +java -jar $snpEff/snpeff.jar +echo "--- varscan ---" +java -jar $varScan + exit 0 ## ----------
--- a/falco.xml Thu Sep 11 06:59:12 2014 -0400 +++ b/falco.xml Thu Sep 11 10:49:52 2014 -0400 @@ -9,6 +9,8 @@ <requirement type="package" version="2">bcftools</requirement> <!-- --> + <requirement type="set_environment">JAVA_JAR_PATH</requirement> + <requirement type="set_environment">SNPEFF_JAR_PATH</requirement> <requirement type="set_environment">TOOL_DIR</requirement> </requirements>
--- a/tool_dependencies.xml Thu Sep 11 06:59:12 2014 -0400 +++ b/tool_dependencies.xml Thu Sep 11 10:49:52 2014 -0400 @@ -33,4 +33,6 @@ <readme>Let's see where this msg appears...ENV VAR</readme> </set_environment> + <!--<environment_variable action="set_to" name="VARSCAN_DIR">$JAVA_JAR_PATH</environment_variable>--> + </tool_dependency>