Mercurial > repos > biomonika > linkyx
changeset 1:38fbf97cfce2
new dependencies
author | biomonika <biomonika@psu.edu> |
---|---|
date | Tue, 02 Sep 2014 15:09:32 -0400 |
parents | 1955f03f092e |
children | c35c3c6a543e |
files | README tool_dependencies.xml |
diffstat | 2 files changed, 35 insertions(+), 15 deletions(-) [+] |
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--- a/README Tue Sep 02 14:16:04 2014 -0400 +++ b/README Tue Sep 02 15:09:32 2014 -0400 @@ -1,19 +1,14 @@ LinkYX -The pipeline can be executed by the following command: - -./runLinkYX.sh email@email.com hostname - -Please, make sure that all paths in config_devel are set accordingly. -Otherwise, use online version available from https://perun.metacentrum.cz/perun-registrar-non/?vo=linkYX +Fully automated pipeline for detection of sex linked genes using RNA-Seq data +bitbucket.org/biomonika/linkyx -Also, make sure that the input files are copied into the folder named 'input' and follow naming conventions: -mother_1.fastx, mother_2.fastx -father_1.fastx, mother_2.fastx -daughter_1.fastx, daughter_2.fastx -son_1.fastx, son_2.fastx +Please install following dependencies from toolshed: +toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4 +toolshed.g2.bx.psu.edu/repos/bhaas/trinityrnaseq/trinityrnaseq/0.0.1 +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 -Instead of fastx, use fastq or fasta format, depending on the type of your -data. If only single-end reads are used, do not upload the second file. - -If you have any questions, please use following email address: michalovova.monika@gmail.com \ No newline at end of file +If you have any questions, please use following email address: biomonika@psu.edu \ No newline at end of file
--- a/tool_dependencies.xml Tue Sep 02 14:16:04 2014 -0400 +++ b/tool_dependencies.xml Tue Sep 02 15:09:32 2014 -0400 @@ -37,4 +37,29 @@ Bundle::BioPerl </readme> </package> + + <package name="fastq_groomer" version="1.0.4"> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="fastq_groomer" owner="devteam" changeset_revision="a347750db1d1" /> + </package> + + <package name="trinityrnaseq" version="0.0.1"> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="trinityrnaseq" owner="bhaas" changeset_revision="a347750db1d1" /> + </package> + + <package name="bwa_wrappers" version="1.2.3"> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="bwa_wrapper" owner="devteam" changeset_revision="a347750db1d1" /> + </package> + + <package name="sam_to_bam" version="1.1.4"> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="sam_to_bam" owner="devteam" changeset_revision="a347750db1d1" /> + </package> + + <package name="samtools_sort" version="1.0.2"> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="samtools_sort" owner="iuc" changeset_revision="a347750db1d1" /> + </package> + + <package name="picard" version="1.56.0"> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="rgPicardMarkDups" owner="devteam" changeset_revision="a347750db1d1" /> + </package> + </tool_dependency> \ No newline at end of file