Mercurial > repos > stef > falco
changeset 30:3419fc808193 draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 10 Oct 2014 06:33:58 -0400 |
| parents | 02e5aee670de |
| children | c7203abb7040 |
| files | falco-call.xml falco/init.sh tool_dependencies.xml |
| diffstat | 3 files changed, 8 insertions(+), 5 deletions(-) [+] |
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--- a/falco-call.xml Fri Oct 10 06:28:46 2014 -0400 +++ b/falco-call.xml Fri Oct 10 06:33:58 2014 -0400 @@ -3,12 +3,12 @@ <requirements> <requirement type="package" version="0.1.19">samtools</requirement> - <requirement type="package" version="3.1.0">R</requirement> + <requirement type="package" version="2">bcftools</requirement> <!-- <requirement type="package" version="3.4">snpeff</requirement> <requirement type="package" version="2">varscan</requirement> - <requirement type="package" version="2">bcftools</requirement> + --> <!--
--- a/falco/init.sh Fri Oct 10 06:28:46 2014 -0400 +++ b/falco/init.sh Fri Oct 10 06:33:58 2014 -0400 @@ -24,13 +24,15 @@ #qTrim=/ccagc/bin/fastq_quality_trimmer #stampy=/ccagc/lib/stampy/stampy-1.0.18/stampy.py #samtools=/ccagc/lib/samtools/samtools-0.1.18/samtools +samtools=samtools #bcftools=/ccagc/lib/samtools/samtools-0.1.18/bcftools/bcftools +bcftools=bcftools #snpEff=/ccagc/lib/snpEff/snpEff_3_0a #snpEff=/ccagc/lib/snpEff/snpEff_v3_4 #snpSift=/ccagc/lib/SnpSift #varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar -java=/usr/bin/java +#java=/usr/bin/java #bwa=/ccagc/lib/bwa/bwa-0.5.9/bwa #flash=/ccagc/lib/flash/FLASH-1.2.2/flash
--- a/tool_dependencies.xml Fri Oct 10 06:28:46 2014 -0400 +++ b/tool_dependencies.xml Fri Oct 10 06:33:58 2014 -0400 @@ -10,12 +10,13 @@ <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <!-- + <package name="bcftools" version="2"> - <repository name="bcftools" owner="iuc" prior_installation_required="TRUE" /> + <repository changeset_revision="5f9ba601748e" name="bcftools" owner="iuc" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <readme>Let's see where this msg appears...bcftools</readme> </package> + <!-- <package name="snpeff" version="3.4"> <repository name="package_snpeff_3_4" owner="jjohnson" prior_installation_required="TRUE" /> <readme>Let's see where this msg appears...snpeff</readme>