diff --git a/scripts/fetch_eggs.py b/scripts/fetch_eggs.py index 6c29c711879..871bc04c466 100755 --- a/scripts/fetch_eggs.py +++ b/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: diff --git a/scripts/get_platforms.py b/scripts/get_platforms.py index 3bccb74992b..9b680d628a4 100755 --- a/scripts/get_platforms.py +++ b/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 ) diff --git a/tools/annotation_profiler/annotation_profiler.xml b/tools/annotation_profiler/annotation_profiler.xml index 8e267939430..d461d867f8a 100644 --- a/tools/annotation_profiler/annotation_profiler.xml +++ b/tools/annotation_profiler/annotation_profiler.xml @@ -1,6 +1,6 @@ for a set of genomic intervals - 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 + 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