Mercurial > repos > biomonika > linkyx
changeset 20:ea52ef8d7f3a
added perl dependency since galaxy A seems working and added samtools sort
author | biomonika <biomonika@psu.edu> |
---|---|
date | Thu, 11 Sep 2014 19:17:11 -0400 |
parents | 05e63b38b6ee |
children | 55a373f7e669 |
files | LINKYX_mpileup_wrapper.sh LINKYX_mpileup_wrapper.xml README.txt sort_bam.sh sort_bam.xml tool_dependencies.xml |
diffstat | 6 files changed, 46 insertions(+), 14 deletions(-) [+] |
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--- a/LINKYX_mpileup_wrapper.sh Wed Sep 10 20:07:52 2014 -0400 +++ b/LINKYX_mpileup_wrapper.sh Thu Sep 11 19:17:11 2014 -0400 @@ -5,8 +5,4 @@ sorted_bam=${bam_file}_sorted -#LINKYX_PATH set during toolshed installation - samtools mpileup -uf $reference $bam_file 2>log.txt | bcftools view -p 0.85 -cgv - 2>log.txt >$results - -#samtools mpileup -uf $reference $2 2>log.txt | bcftools view -p 0.85 -cgv - 2>>log.txt| vcfutils.pl varFilter >$results 2>>log.txt \ No newline at end of file
--- a/LINKYX_mpileup_wrapper.xml Wed Sep 10 20:07:52 2014 -0400 +++ b/LINKYX_mpileup_wrapper.xml Thu Sep 11 19:17:11 2014 -0400 @@ -22,7 +22,7 @@ </tests> <help> - This tool tests if primers are present in gorilla female or on human Y or chimp Y chromosome. + Run mpileup with LINKYX-specific parameters </help> </tool> \ No newline at end of file
--- a/README.txt Wed Sep 10 20:07:52 2014 -0400 +++ b/README.txt Thu Sep 11 19:17:11 2014 -0400 @@ -1,14 +1,13 @@ LinkYX Fully automated pipeline for detection of sex linked genes using RNA-Seq data -bitbucket.org/biomonika/linkyx + +The installation is described on the project wiki page: +https://bitbucket.org/biomonika/linkyx/wiki/Home -Please install following dependencies from toolshed: -toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4 -testtoolshed.g2.bx.psu.edu/view/jjohnson/trinityrnaseq/0.0.2 -toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 -toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4 -toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2 -toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0 +In order to install additional tools used in the workflow, please install following repository suite definition to the Galaxy: +https://testtoolshed.g2.bx.psu.edu/view/marten/suite_linkyx_bundle_0_1 + +Code repositary: bitbucket.org/biomonika/linkyx If you have any questions, please use following email address: biomonika@psu.edu \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sort_bam.sh Thu Sep 11 19:17:11 2014 -0400 @@ -0,0 +1,6 @@ +#!/bin/bash +results=$1; +bam_file=$2; + +samtools sort $bam_file $results 2>log.txt +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sort_bam.xml Thu Sep 11 19:17:11 2014 -0400 @@ -0,0 +1,26 @@ +<tool id="sort_bam" name="sort_bam"> + <description>Sort bam file based on chromosomal coordinates.</description> + <requirements> + <requirement type="set_environment">LINKYX_PATH</requirement> + <requirement type="set_environment">SAMTOOLS</requirement> + <requirement type="package" version="0.1.19">samtools</requirement> + <requirement type="package" version="1.6.922">bioperl</requirement> + </requirements> + <command interpreter="bash">sort_bam.sh $output $input1</command> + <inputs> + <param format="bam" name="input1" type="data" label="Alignment file"/> + </inputs> + <outputs> + <data format="bam" name="output" /> + </outputs> + + <tests> + <test> + </test> + </tests> + + <help> + Sort bam file based on chromosomal coordinates. + </help> + + </tool> \ No newline at end of file
--- a/tool_dependencies.xml Wed Sep 10 20:07:52 2014 -0400 +++ b/tool_dependencies.xml Thu Sep 11 19:17:11 2014 -0400 @@ -18,11 +18,16 @@ <readme>Compiling samtools with fPIC in order to create bam.h and compiled libbam.a files</readme> </package> + <package name="perl" version="5.18.1"> + <repository name="package_perl_5_18" owner="iuc" prior_installation_required="True" /> + </package> + <package name="bioperl" version="1.6.922"> <install version="1.0"> <actions> <action type="setup_perl_environment"> - <repository changeset_revision="a1a111b9faa5" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <package name="perl" version="5.18.1" /> </repository> <!-- allow downloading and installing an Perl package from cpan.org--> <package>XML::Parser</package>