# HG changeset patch
# User devteam
# Date 1426704575 14400
# Node ID bed5e31494e45a32455975f43c6750acb3f83855
Uploaded
diff -r 000000000000 -r bed5e31494e4 .shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml Wed Mar 18 14:49:35 2015 -0400
@@ -0,0 +1,4 @@
+# repository published to https://toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder
+owner: devteam
+name: data_manager_bwa_mem_index_builder
+
diff -r 000000000000 -r bed5e31494e4 data_manager/bwa_mem_index_builder.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bwa_mem_index_builder.py Wed Mar 18 14:49:35 2015 -0400
@@ -0,0 +1,90 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+import sys
+import os
+import tempfile
+import optparse
+import subprocess
+
+from json import loads, dumps
+
+
+CHUNK_SIZE = 2**20
+TWO_GB = 2**30*2
+
+DEFAULT_DATA_TABLE_NAME = "bwa_mem_indexes"
+
+def get_id_name( params, dbkey, fasta_description=None):
+ #TODO: ensure sequence_id is unique and does not already appear in location file
+ sequence_id = params['param_dict']['sequence_id']
+ if not sequence_id:
+ sequence_id = dbkey
+
+ sequence_name = params['param_dict']['sequence_name']
+ if not sequence_name:
+ sequence_name = fasta_description
+ if not sequence_name:
+ sequence_name = dbkey
+ return sequence_id, sequence_name
+
+def build_bwa_index( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ):
+ #TODO: allow multiple FASTA input files
+ #tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-bwa-index-builder-' )
+ fasta_base_name = os.path.split( fasta_filename )[-1]
+ sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
+ os.symlink( fasta_filename, sym_linked_fasta_filename )
+ if params['param_dict']['index_algorithm'] == 'automatic':
+ if os.stat( fasta_filename ).st_size < TWO_GB: #use 2 GB as cut off for memory vs. max of 2gb database size; this is somewhat arbitrary
+ index_algorithm = 'is'
+ else:
+ index_algorithm = 'bwtsw'
+ else:
+ index_algorithm = params['param_dict']['index_algorithm']
+
+ args = [ 'bwa', 'index', '-a', index_algorithm ]
+ args.append( sym_linked_fasta_filename )
+ proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
+ return_code = proc.wait()
+ if return_code:
+ print >> sys.stderr, "Error building index."
+ sys.exit( return_code )
+ data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
+ _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
+
+def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
+ data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+ data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
+ data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
+ return data_manager_dict
+
+def main():
+ #Parse Command Line
+ parser = optparse.OptionParser()
+ parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
+ parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
+ parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
+ parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' )
+ (options, args) = parser.parse_args()
+
+ filename = args[0]
+
+ params = loads( open( filename ).read() )
+ target_directory = params[ 'output_data' ][0]['extra_files_path']
+ os.mkdir( target_directory )
+ data_manager_dict = {}
+
+ dbkey = options.fasta_dbkey
+
+ if dbkey in [ None, '', '?' ]:
+ raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
+
+ sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description )
+
+ #build the index
+ build_bwa_index( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME )
+
+ #save info to json file
+ open( filename, 'wb' ).write( dumps( data_manager_dict ) )
+
+if __name__ == "__main__": main()
diff -r 000000000000 -r bed5e31494e4 data_manager/bwa_mem_index_builder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bwa_mem_index_builder.xml Wed Mar 18 14:49:35 2015 -0400
@@ -0,0 +1,37 @@
+
+ builder
+
+ bwa
+
+ bwa_mem_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "bwa_mem_indexes"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+
+
+
diff -r 000000000000 -r bed5e31494e4 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Wed Mar 18 14:49:35 2015 -0400
@@ -0,0 +1,22 @@
+
+
+
+
+
+
+
+
diff -r 000000000000 -r bed5e31494e4 tool-data/bwa_mem_index.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bwa_mem_index.loc.sample Wed Mar 18 14:49:35 2015 -0400
@@ -0,0 +1,38 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of BWA indexed sequences data files. You will need
+#to create these data files and then create a bwa_index.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bwa_index.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had phiX indexed stored in
+#/depot/data2/galaxy/phiX/base/,
+#then the bwa_index.loc entry would look like this:
+#
+#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
+#
+#and your /depot/data2/galaxy/phiX/base/ directory
+#would contain phiX.fa.* files:
+#
+#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb
+#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann
+#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt
+#...etc...
+#
+#Your bwa_index.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
+#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
+#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
diff -r 000000000000 -r bed5e31494e4 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Mar 18 14:49:35 2015 -0400
@@ -0,0 +1,7 @@
+
+
+
+ value, dbkey, name, path
+
+
+
diff -r 000000000000 -r bed5e31494e4 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed Mar 18 14:49:35 2015 -0400
@@ -0,0 +1,6 @@
+
+
+
+
+
+