Mercurial > repos > stef > qdnaseq_test
changeset 3:41387ffa145f draft
Uploaded
author | stef |
---|---|
date | Fri, 05 Sep 2014 11:06:01 -0400 |
parents | 1f17446203d8 |
children | 4f5fd8b917eb |
files | QDNAseq.xml tool_dependencies.xml |
diffstat | 2 files changed, 8 insertions(+), 8 deletions(-) [+] |
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--- a/QDNAseq.xml Fri Sep 05 10:41:06 2014 -0400 +++ b/QDNAseq.xml Fri Sep 05 11:06:01 2014 -0400 @@ -3,14 +3,13 @@ <requirements> <!-- R 3.1.0 dependency will be used instead when available, now default R is used, see command --> - <requirement type="package" version="3.1.0">R</requirement> + <!-- <requirement type="package" version="3.1.0">R</requirement> --> <!-- <requirement type="package" version="1.0.5">qdnaseq</requirement> --> <requirement type="package" version="0.1.18">samtools</requirement> </requirements> <description>Quantitative copy number abberation detection</description> - <!-- command block to call script with default R installation --> <!-- change to /full/path/to/Rscript if required (eg /ccagc/lib/R/R-3.1.0/bin/Rscript) --> <command interpreter="Rscript"> QDNAseq.R @@ -38,9 +37,9 @@ <!-- Bin Size: only certain sizes are supported by QDNAseq package --> <param name="binSizes" type="select" optional="false" multiple="true" label="Select bin-sizes to use (kb)" help="Larger bin sizes provide faster analysis but lower resolution"> <option value="1000" selected="true">1Mb</option> - <option value="100">100kb</option> + <option value="100" selected="true">100kb</option> <option value="30">30kb</option> - <option value="15">15kb</option> + <option value="15" selected="true">15kb</option> <option value="5">5kb</option> <option value="1">1kb</option> </param>
--- a/tool_dependencies.xml Fri Sep 05 10:41:06 2014 -0400 +++ b/tool_dependencies.xml Fri Sep 05 11:06:01 2014 -0400 @@ -5,20 +5,21 @@ <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="TRUE" /> </package> - <!-- As soon as R 3_1_0 package works, all QDNAseq dependencies will be set via "package_qdnaseq_1_0_5" --> - <!-- Now this depency has to be manually installed by installing Bioconductor package "QDNAseq" --> + <!-- As soon as R 3_1_0 package works good, all dependencies will be set via "package_qdnaseq_1_0_5" --> + <!-- Currently these have to be manually installed by installing Bioconductor package "QDNAseq" --> + <!-- <package name="R" version="3.1.0"> <repository changeset_revision="a6cc7706ea14" name="package_r_3_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" prior_installation_required="TRUE" /> </package> - + --> + <!-- <package name="qdnaseq" version="1.0.5"> <repository name="package_qdnaseq_1_0_5" owner="stef"/> </package> --> - <!-- environment variable not in use now --> <!-- <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>