merge

scripts/fetch_eggs.py

@@ -1,9 +1,13 @@
 """
-usage: fetch_eggs.py [egg_name]
+usage: fetch_eggs.py [egg_name] [platform]
     With no arguments, fetches all eggs necessary according to the
     settings in universe_wsgi.ini.
   egg_name - Fetch only this egg (as defined in eggs.ini) or 'all' for
     all eggs (even those not required by your settings).
+  platform - Fetch eggs for a specific platform (if not provided, fetch
+    eggs for *this* platform).  Useful for fetching eggs for cluster
+    nodes which are of a different architecture than the head node.
+    Platform name can be determined with the get_platforms.py script.
 """
 import os, sys, logging
 
@@ -17,6 +21,8 @@ sys.path.append( lib )
 from galaxy.eggs import *
 
 c = Crate()
+if len( sys.argv ) == 3:
+    c.platform = { 'peak' : sys.argv[2].rsplit('-',1)[0], 'galaxy' : sys.argv[2] }
 c.parse()
 try:
     if len( sys.argv ) == 1:

scripts/get_platforms.py

@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 
-import sys, os
+import os, sys
 
 assert sys.version_info[:2] >= ( 2, 4 )
 
 lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) )
 sys.path.append( lib )
 
-from galaxy.eggs import get_platform, get_noplatform
-print get_noplatform()
-print get_platform( platform=True )
+from galaxy.eggs import get_platform
+print get_platform()
+print get_platform( True )

tools/annotation_profiler/annotation_profiler.xml

@@ -1,6 +1,6 @@
 <tool id="Annotation_Profiler_0" name="Profile Annotations" Version="1.0.0">
   <description>for a set of genomic intervals</description>
-  <command interpreter="python2.4">annotation_profiler_for_interval.py -i $input1 -c ${input1.metadata.chromCol} -s ${input1.metadata.startCol} -e ${input1.metadata.endCol} -o $out_file1 $keep_empty -p /depot/data2/galaxy/annotation_profiler/$dbkey $summary -l ${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey}.len -b 3 -t $table_names</command>
+  <command interpreter="python">annotation_profiler_for_interval.py -i $input1 -c ${input1.metadata.chromCol} -s ${input1.metadata.startCol} -e ${input1.metadata.endCol} -o $out_file1 $keep_empty -p /depot/data2/galaxy/annotation_profiler/$dbkey $summary -l ${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey}.len -b 3 -t $table_names</command>
   <inputs>
     <param format="interval" name="input1" type="data" label="Choose Intervals">
       <validator type="dataset_metadata_in_file" filename="annotation_profiler_valid_builds.txt" metadata_name="dbkey" metadata_column="0" message="Profiling is not currently available for this species."/>