Mercurial > repos > stef > falco
changeset 5:90badfe82b95 draft
Uploaded
author | stef |
---|---|
date | Thu, 11 Sep 2014 06:56:58 -0400 |
parents | f34be89e9674 |
children | cebbd6a92411 |
files | README.rst falco.sh falco/init.sh tool_dependencies.xml tool_dependencies_MAINTOOLSHED.xml |
diffstat | 5 files changed, 14 insertions(+), 47 deletions(-) [+] |
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--- a/README.rst Thu Sep 11 06:40:27 2014 -0400 +++ b/README.rst Thu Sep 11 06:56:58 2014 -0400 @@ -14,15 +14,6 @@ July 2014 * first release in Test Tool Shed ============== ======================================================================== -Tool Versioning -=============== - -Tools will have versions of the form X.Y.Z. Versions -differing only after the second decimal should be completely -compatible with each other. Breaking changes should result in an -increment of the number before and/or after the first decimal. All -tools of version less than 1.0.0 should be considered beta. - Bug Reports & other questions =============================
--- a/falco.sh Thu Sep 11 06:40:27 2014 -0400 +++ b/falco.sh Thu Sep 11 06:56:58 2014 -0400 @@ -64,6 +64,12 @@ echo "HTMLOUT: "$html_out echo "VCFOUT : "$vcf_out echo "INIT : "$init_file +source $init_file +echo "--- sam ---" +samtools +echo "--- bcf ---" +bcftools +exit 0 ## ---------- ## create output files dir
--- a/falco/init.sh Thu Sep 11 06:40:27 2014 -0400 +++ b/falco/init.sh Thu Sep 11 06:56:58 2014 -0400 @@ -23,13 +23,13 @@ adapt_clipper=/ccagc/lib/cutadapt/cutadapt-1.1/bin/cutadapt qTrim=/ccagc/bin/fastq_quality_trimmer stampy=/ccagc/lib/stampy/stampy-1.0.18/stampy.py -samtools=/ccagc/lib/samtools/samtools-0.1.18/samtools -bcftools=/ccagc/lib/samtools/samtools-0.1.18/bcftools/bcftools +#samtools=/ccagc/lib/samtools/samtools-0.1.18/samtools +#bcftools=/ccagc/lib/samtools/samtools-0.1.18/bcftools/bcftools #snpEff=/ccagc/lib/snpEff/snpEff_3_0a -snpEff=/ccagc/lib/snpEff/snpEff_v3_4 -snpSift=/ccagc/lib/SnpSift +#snpEff=/ccagc/lib/snpEff/snpEff_v3_4 +#snpSift=/ccagc/lib/SnpSift -varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar +#varscan=/ccagc/lib/VarScan/VarScan.v2.2.11.jar java=/usr/bin/java bwa=/ccagc/lib/bwa/bwa-0.5.9/bwa flash=/ccagc/lib/flash/FLASH-1.2.2/flash @@ -53,5 +53,5 @@ errorRate=$DIR/misc/errorRate.pl plotQc=$DIR/misc/plotsQC.R -export PATH=$PATH:/ccagc/lib/samtools/samtools-0.1.18/ +#export PATH=$PATH:/ccagc/lib/samtools/samtools-0.1.18/ source ./galaxy_init.sh
--- a/tool_dependencies.xml Thu Sep 11 06:40:27 2014 -0400 +++ b/tool_dependencies.xml Thu Sep 11 06:56:58 2014 -0400 @@ -7,8 +7,8 @@ <readme>Let's see where this msg appears...R</readme> </package> - <package name="samtools" version="0.1.18"> - <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="TRUE" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <readme>Let's see where this msg appears...samtools</readme> </package>
--- a/tool_dependencies_MAINTOOLSHED.xml Thu Sep 11 06:40:27 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - - <package name="R" version="3.0.3"> - <repository name="package_r_3_0_3" toolshed="http://toolshed.g2.bx.psu.edu" owner="iuc" changeset_revision="f386d7431fe0" /> - <readme>Let's see where this msg appears...R</readme> - </package> - - <package name="samtools" version="0.1.18"> - <repository name="package_samtools_0_1_18" toolshed="http://toolshed.g2.bx.psu.edu" owner="devteam" changeset_revision="171cd8bc208d"/> - <readme>Let's see where this msg appears...samtools</readme> - </package> - - <package name="snpeff" version="3.4"> - <repository name="package_snpeff_3_4" toolshed="http://toolshed.g2.bx.psu.edu" owner="iuc" changeset_revision="af7ff8187d09"/> - <readme>Let's see where this msg appears...snpeff</readme> - </package> - - <package name="varscan" version="2"> - <repository name="varscan_version_2" toolshed="http://toolshed.g2.bx.psu.edu" owner="devteam" changeset_revision="6f8cead3dc93"/> - <readme>Let's see where this msg appears...varscan</readme> - </package> - - <!-- TXT --> - <set_environment version="1.0"> - <environment_variable action="set_to" name="TOOL_DIR">$REPOSITORY_INSTALL_DIR</environment_variable> - <readme>Let's see where this msg appears...ENV VAR</readme> - </set_environment> - -</tool_dependency>