changeset 1:23b22c1692fa draft default tip

Replace simplejson with json.
author hackdna
date Tue, 20 May 2014 10:53:35 -0400
parents b15734276ca3
children
files run_spp.R spp_wrapper.py spp_wrapper.xml
diffstat 3 files changed, 6 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/run_spp.R	Thu Oct 17 12:39:45 2013 -0400
+++ b/run_spp.R	Tue May 20 10:53:35 2014 -0400
@@ -120,7 +120,7 @@
 	sep.peak <- NA # user-defined peak shift
 	exclude.min <- 10 # lowerbound of strand shift exclusion region
 	exclude.max <- NaN # upperbound of strand shift exclusion region
-	n.nodes <- NA # number of parallel processing nodes
+	n.nodes <- 32 # number of parallel processing nodes
 	fdr <- 0.01 # false discovery rate threshold for peak calling
 	npeak <- NA # threshold on number of peaks to call
 	temp.dir <- tempdir() # temporary directory
--- a/spp_wrapper.py	Thu Oct 17 12:39:45 2013 -0400
+++ b/spp_wrapper.py	Tue May 20 10:53:35 2014 -0400
@@ -5,14 +5,12 @@
 
 import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip
 from galaxy import eggs
-import pkg_resources
-pkg_resources.require( "simplejson" )
-import simplejson
+import json
 
 CHUNK_SIZE = 1024
 
 def main():
-    options = simplejson.load( open( sys.argv[1] ) )
+    options = json.load( open( sys.argv[1] ) )
     output_narrow_peak = sys.argv[2]
     output_region_peak = sys.argv[3]
     output_peakshift_file = sys.argv[4]
@@ -99,4 +97,4 @@
     os.unlink( stderr_name )
     #os.rmdir( tmp_dir )
 
-if __name__ == "__main__": main()
\ No newline at end of file
+if __name__ == "__main__": main()
--- a/spp_wrapper.xml	Thu Oct 17 12:39:45 2013 -0400
+++ b/spp_wrapper.xml	Tue May 20 10:53:35 2014 -0400
@@ -99,7 +99,7 @@
 
   <configfiles>
     <configfile name="options_file">&lt;%
-import simplejson
+import json
 %&gt;
 #set $__options ={ 'experiment_name':str($experiment_name), 'chip_file':str($major_command.input_chipseq_file1) }
 
@@ -165,7 +165,7 @@
         #set $__options['savp'] = str( $major_command.save_plot_file ) 
 #end if
 
-${ simplejson.dumps( __options ) }
+${ json.dumps( __options ) }
     </configfile>
   </configfiles>
   <tests>
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