Mercurial > repos > ryo-tas > macs14
changeset 4:fdb73ac17c47
commit
| author | pitagora <yamanaka@genome.rcast.u-tokyo.ac.jp> |
|---|---|
| date | Wed, 22 Oct 2014 12:41:58 +0900 |
| parents | cdd9791c0afa |
| children | 93dbf00c92d3 |
| files | macs14_wrapper.py macs14_wrapper.xml tool_dependencies.xml |
| diffstat | 3 files changed, 14 insertions(+), 8 deletions(-) [+] |
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--- a/macs14_wrapper.py Mon Feb 13 02:38:59 2012 -0500 +++ b/macs14_wrapper.py Wed Oct 22 12:41:58 2014 +0900 @@ -1,8 +1,9 @@ import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip -from galaxy import eggs +#from galaxy import eggs import pkg_resources -pkg_resources.require( "simplejson" ) -import simplejson +#pkg_resources.require( "simplejson" ) +#import simplejson +import json CHUNK_SIZE = 1024 @@ -42,7 +43,7 @@ out.close() def main(): - options = simplejson.load( open( sys.argv[1] ) ) + options = json.load( open( sys.argv[1] ) ) output_bed = sys.argv[2] output_extra_html = sys.argv[3] output_extra_path = sys.argv[4]
--- a/macs14_wrapper.xml Mon Feb 13 02:38:59 2012 -0500 +++ b/macs14_wrapper.xml Wed Oct 22 12:41:58 2014 +0900 @@ -1,9 +1,8 @@ -<tool id="peakcalling_macs14" name="MACS14" version="1.4.1"> - <description>Model-based Analysis of ChIP-Seq (1.4.1)</description> +<tool id="peakcalling_macs14" name="MACS14" version="1.0.0"> + <description>Model-based Analysis of ChIP-Seq (1.4.2)</description> <command interpreter="python">macs14_wrapper.py $options_file $output_bed_file $output_extra_files $output_extra_files.files_path</command> <requirements> - <requirement type="python-module">macs14</requirement> - <requirement type="package">macs14</requirement> + <requirement type="package" version="2.15.0">R</requirement> </requirements> <inputs> <param name="experiment_name" type="text" value="MACS14 in Galaxy" size="50" label="Experiment Name"/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Oct 22 12:41:58 2014 +0900 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="2.15.0"> + <repository changeset_revision="8ab0d08a3da1" name="package_r_2_15_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>