# HG changeset patch # User iuc # Date 1501920121 14400 # Node ID 6843a0db2da00b86303df4a31bf31c7937583017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380 diff -r 000000000000 -r 6843a0db2da0 data_manager/kallisto_index_builder.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kallisto_index_builder.py Sat Aug 05 04:02:01 2017 -0400 @@ -0,0 +1,82 @@ +#!/usr/bin/env python +# Based heavily on the Bowtie 2 data manager wrapper script by Dan Blankenberg +from __future__ import print_function + +import argparse +import os +import subprocess +import sys +from json import dumps, loads + +DEFAULT_DATA_TABLE_NAME = "kallisto_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_kallisto_index( data_manager_dict, options, params, sequence_id, sequence_name ): + data_table_name = options.data_table_name or DEFAULT_DATA_TABLE_NAME + target_directory = params[ 'output_data' ][0]['extra_files_path'] + if not os.path.exists( target_directory ): + os.mkdir( target_directory ) + fasta_base_name = os.path.split( options.fasta_filename )[-1] + sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) + os.symlink( options.fasta_filename, sym_linked_fasta_filename ) + args = [ 'kallisto', 'index' ] + args.extend( [ sym_linked_fasta_filename, '-i', sequence_id ] ) + proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) + return_code = proc.wait() + if return_code: + print("Error building index.", file=sys.stderr) + sys.exit( return_code ) + data_table_entry = dict( value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id ) + _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 = argparse.ArgumentParser() + parser.add_argument( '--output', dest='output', action='store', type=str, default=None ) + parser.add_argument( '--fasta_filename', dest='fasta_filename', action='store', type=str, default=None ) + parser.add_argument( '--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None ) + parser.add_argument( '--fasta_description', dest='fasta_description', action='store', type=str, default=None ) + parser.add_argument( '--data_table_name', dest='data_table_name', action='store', type=str, default='kallisto_indexes' ) + options = parser.parse_args() + + filename = options.output + + params = loads( open( filename ).read() ) + data_manager_dict = {} + + if options.fasta_dbkey in [ None, '', '?' ]: + raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) ) + + sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description ) + + # build the index + build_kallisto_index( data_manager_dict, options, params, sequence_id, sequence_name ) + + # save info to json file + open( filename, 'w' ).write( dumps( data_manager_dict ) ) + + +if __name__ == "__main__": + main() diff -r 000000000000 -r 6843a0db2da0 data_manager/kallisto_index_builder.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kallisto_index_builder.xml Sat Aug 05 04:02:01 2017 -0400 @@ -0,0 +1,51 @@ + + index builder + + kallisto + + + + + + + + + + + + + + +`__ is a program for +quantifying abundances of transcripts from RNA-Seq data, or more generally of +target sequences using high-throughput sequencing reads. It is based on the +novel idea of pseudoalignment for rapidly determining the compatibility of +reads with targets, without the need for alignment. On benchmarks with standard +RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 +minutes on a Mac desktop computer using only the read sequences and a +transcriptome index that itself takes less than 10 minutes to build. +Pseudoalignment of reads preserves the key information needed for +quantification, and kallisto is therefore not only fast, but also as accurate +as existing quantification tools. In fact, because the pseudoalignment +procedure is robust to errors in the reads, in many benchmarks kallisto +significantly outperforms existing tools. +]]> + + + 10.1038/nmeth.3317 + + diff -r 000000000000 -r 6843a0db2da0 data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Sat Aug 05 04:02:01 2017 -0400 @@ -0,0 +1,20 @@ + + + + + + + + + + + + ${dbkey}/kallisto_index/${value} + + ${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/kallisto_index/${value}/${path} + abspath + + + + + \ No newline at end of file diff -r 000000000000 -r 6843a0db2da0 tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Sat Aug 05 04:02:01 2017 -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 6843a0db2da0 tool-data/kallisto_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/kallisto_indexes.loc.sample Sat Aug 05 04:02:01 2017 -0400 @@ -0,0 +1,33 @@ +# kallisto_indexes.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 kallisto. +# 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 kallisto_indexes.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 sacCer3 indexes stored in: +# +# /depot/data2/galaxy/sacCer3/kallisto_indexes/ +# +# containing sacCer3 genome and sacCer3.*.ht2 files, such as: +# +# -rw-rw-r-- 1 dave dave 12M Sep 23 13:57 sacCer3.fa +# -rw-rw-r-- 1 dave dave 2.9M Sep 23 13:57 sacCer3.kallisto +# +# then the kallisto_indexes.loc entry could look like this: +# +#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/kallisto_indexes/sacCer3.kallisto +# +#More examples: +# +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/kallisto_indexes/mm10 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/kallisto_indexes/dm3 +# +# diff -r 000000000000 -r 6843a0db2da0 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sat Aug 05 04:02:01 2017 -0400 @@ -0,0 +1,13 @@ + + + + + value, dbkey, name, path + +
+ + + value, dbkey, name, path + +
+