# HG changeset patch # User jjohnson # Date 1377014307 14400 # Node ID 5515ee3559f00c4273a0de240d14e0d2102b22ca Uploaded diff -r 000000000000 -r 5515ee3559f0 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue Aug 20 11:58:27 2013 -0400 @@ -0,0 +1,2 @@ +Builds a bowtie version 2 index from a fasta reference from the tool_data_table_conf all_fasta reference. +It adds an entry to the tool_data_table_conf bowtie2_indexes reference. diff -r 000000000000 -r 5515ee3559f0 data_manager/bowtie2_index_builder.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/bowtie2_index_builder.py Tue Aug 20 11:58:27 2013 -0400 @@ -0,0 +1,88 @@ +#!/usr/bin/env python + +import sys +import os +import tempfile +import optparse +import subprocess + +from galaxy.util.json import from_json_string, to_json_string + + +CHUNK_SIZE = 2**20 + +DEFAULT_DATA_TABLE_NAME = "bowtie2_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_bowtie_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-bowtie2-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 ) + args = [ 'bowtie2-build',sym_linked_fasta_filename,fasta_base_name ] + tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-bowtie2-index-builder-stderr" ) + proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) + return_code = proc.wait() + if return_code: + tmp_stderr.flush() + tmp_stderr.seek(0) + print >> sys.stderr, "Error building index:" + while True: + chunk = tmp_stderr.read( CHUNK_SIZE ) + if not chunk: + break + sys.stderr.write( chunk ) + sys.exit( return_code ) + tmp_stderr.close() + 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 = from_json_string( 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_bowtie_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( to_json_string( data_manager_dict ) ) + +if __name__ == "__main__": main() diff -r 000000000000 -r 5515ee3559f0 data_manager/bowtie2_index_builder.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/bowtie2_index_builder.xml Tue Aug 20 11:58:27 2013 -0400 @@ -0,0 +1,25 @@ + + bowtie2 index builder + + bowtie + + bowtie2_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 "bowtie2_indexes" + + + + + + + + + + + + + +.. class:: infomark + +**Notice:** If you leave name, description, or id blank, it will be generated automatically. + + + diff -r 000000000000 -r 5515ee3559f0 data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Tue Aug 20 11:58:27 2013 -0400 @@ -0,0 +1,22 @@ + + + + + + + + + + + + + ${dbkey}/bowtie2_index + + ${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bowtie2_index/${path} + abspath + + + + + + diff -r 000000000000 -r 5515ee3559f0 tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Tue Aug 20 11:58:27 2013 -0400 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +# +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# diff -r 000000000000 -r 5515ee3559f0 tool-data/bowtie2_indices.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bowtie2_indices.loc.sample Tue Aug 20 11:58:27 2013 -0400 @@ -0,0 +1,37 @@ +# bowtie2_indices.loc.sample +# This is a *.loc.sample file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2. +# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup +# First create these data files and save them in your own data directory structure. +# Then, create a bowtie_indices.loc file to use those indexes with tools. +# Copy this file, save it with the same name (minus the .sample), +# follow the format examples, and store the result in this directory. +# The file should include an one line entry for each index set. +# The path points to the "basename" for the set, not a specific file. +# It has four text columns seperated by TABS. +# +# +# +# So, for example, if you had hg18 indexes stored in: +# +# /depot/data2/galaxy/hg19/bowtie2/ +# +# containing hg19 genome and hg19.*.bt2 files, such as: +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 +# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 +# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 +# +# then the bowtie2_indices.loc entry could look like this: +# +#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon +# +#More examples: +# +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3 +# +# diff -r 000000000000 -r 5515ee3559f0 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Aug 20 11:58:27 2013 -0400 @@ -0,0 +1,12 @@ + + + + value, dbkey, name, path + +
+ + + value, dbkey, name, path + +
+ diff -r 000000000000 -r 5515ee3559f0 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Aug 20 11:58:27 2013 -0400 @@ -0,0 +1,6 @@ + + + + + +