| Previous changeset 0:6cd60ba8a842 (2018-08-14) Next changeset 2:f7d9182bdcab (2018-10-19) |
|
Commit message:
Uploaded |
|
modified:
data_manager_conf.xml tool_data_table_conf.xml.sample |
|
added:
.shed.yml data_manager/salmon_index_builder.py data_manager/salmon_index_builder.xml tool-data/all_fasta.loc.sample tool-data/salmon_indexes.loc.sample |
|
removed:
README.md data_manager/data_manager_fetch_gff.py data_manager/data_manager_fetch_gff.xml tool-data/all_gff.loc.sample tool-data/representative_gff.loc.sample |
| b |
| diff -r 6cd60ba8a842 -r c5dea2080109 .shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Tue Aug 14 11:19:49 2018 -0400 |
| b |
| @@ -0,0 +1,19 @@ +categories: +- Data Managers +description: Pre-generate indexes for Salmon +homepage_url: https://github.com/COMBINE-lab/salmon +long_description: | + Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimates from RNA-seq data. + Salmon achieves is accuracy and speed via a number of different innovations, + including the use of quasi-mapping (accurate but fast-to-compute proxies for traditional read alignments), + and massively-parallel stochastic collapsed variational inference. + The result is a versatile tool that fits nicely into many differnt pipelines. + For example, you can choose to make use of our quasi-mapping algorithm by providing + Salmon with raw sequencing reads, or, if it is more convenient, you can provide + Salmon with regular alignments (e.g. an unsorted BAM file produced with your favorite aligner), + and it will use the same wicked-fast, state-of-the-art inference algorithm to estimate transcript-level abundances for your experiment. +name: data_manager_salmon_index_builder +owner: iuc +remote_repository_url: https://github.com/ieguinoa/data_manager_salmon_index_builder +type: unrestricted |
| b |
| diff -r 6cd60ba8a842 -r c5dea2080109 README.md --- a/README.md Tue Aug 14 11:14:52 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -# data_manager_fetch_gff -Galaxy Data Manager to fetch gene annotation files |
| b |
| diff -r 6cd60ba8a842 -r c5dea2080109 data_manager/data_manager_fetch_gff.py --- a/data_manager/data_manager_fetch_gff.py Tue Aug 14 11:14:52 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,445 +0,0 @@\n-#!/usr/bin/env python\n-#Dan Blankenberg\n-\n-import sys\n-import os\n-import tempfile\n-import shutil\n-import optparse\n-from ftplib import FTP\n-import tarfile\n-import zipfile\n-import gzip\n-import bz2\n-try:\n- # For Python 3.0 and later\n- from urllib.request import urlopen\n- from io import BytesIO as StringIO\n- from io import UnsupportedOperation\n-except ImportError:\n- # Fall back to Python 2\'s urllib2\n- from urllib2 import urlopen\n- from StringIO import StringIO\n- UnsupportedOperation = AttributeError\n-from json import loads, dumps\n-\n-\n-CHUNK_SIZE = 2**20 # 1mb\n-\n-DATA_TABLE_NAME = \'all_gff\'\n-\n-def cleanup_before_exit( tmp_dir ):\n- if tmp_dir and os.path.exists( tmp_dir ):\n- shutil.rmtree( tmp_dir )\n-\n-\n-def stop_err(msg):\n- sys.stderr.write(msg)\n- sys.exit(1)\n-\n-\n-def get_dbkey_dbname_id_name( params, dbkey_description=None ):\n-# dbkey = params[\'param_dict\'][\'dbkey_source\'][\'dbkey\']\n- #TODO: ensure sequence_id is unique and does not already appear in location file\n- sequence_id = params[\'param_dict\'][\'sequence_id\']\n- if not sequence_id:\n- sequence_id = dbkey #uuid.uuid4() generate and use an uuid instead?\n- \n-# if params[\'param_dict\'][\'dbkey_source\'][\'dbkey_source_selector\'] == \'new\':\n-# dbkey_name = params[\'param_dict\'][\'dbkey_source\'][\'dbkey_name\']\n-# if not dbkey_name:\n-# dbkey_name = dbkey\n-# else:\n-# dbkey_name = None\n- dbkey = params[\'param_dict\'][\'dbkey\'] \n- dbkey_name = dbkey_description\n- sequence_name = params[\'param_dict\'][\'sequence_name\']\n- if not sequence_name:\n- sequence_name = dbkey_description\n- if not sequence_name:\n- sequence_name = dbkey\n- return dbkey, dbkey_name, sequence_id, sequence_name\n-\n-\n-def _get_files_in_ftp_path( ftp, path ):\n- path_contents = []\n- ftp.retrlines( \'MLSD %s\' % ( path ), path_contents.append )\n- return [ line.split( \';\' )[ -1 ].lstrip() for line in path_contents ]\n-\n-\n-def _get_stream_readers_for_tar( fh, tmp_dir ):\n- fasta_tar = tarfile.open( fileobj=fh, mode=\'r:*\' )\n- return [x for x in [fasta_tar.extractfile(member) for member in fasta_tar.getmembers()] if x]\n-\n-\n-def _get_stream_readers_for_zip( fh, tmp_dir ):\n- """\n- Unpacks all archived files in a zip file.\n- Individual files will be concatenated (in _stream_fasta_to_file)\n- """\n- fasta_zip = zipfile.ZipFile( fh, \'r\' )\n- rval = []\n- for member in fasta_zip.namelist():\n- fasta_zip.extract( member, tmp_dir )\n- rval.append( open( os.path.join( tmp_dir, member ), \'rb\' ) )\n- return rval\n-\n-\n-def _get_stream_readers_for_gzip( fh, tmp_dir ):\n- return [ gzip.GzipFile( fileobj=fh, mode=\'rb\') ]\n-\n-\n-def _get_stream_readers_for_bz2( fh, tmp_dir ):\n- return [ bz2.BZ2File( fh.name, \'rb\') ]\n-\n-\n-def sort_fasta( fasta_filename, sort_method, params ):\n- if sort_method is None:\n- return\n- assert sort_method in SORTING_METHODS, ValueError( "%s is not a valid sorting option." % sort_method )\n- return SORTING_METHODS[ sort_method ]( fasta_filename, params )\n-\n-\n-def _move_and_index_fasta_for_sorting( fasta_filename ):\n- unsorted_filename = tempfile.NamedTemporaryFile().name\n- shutil.move( fasta_filename, unsorted_filename )\n- fasta_offsets = {}\n- unsorted_fh = open( unsorted_filename )\n- while True:\n- offset = unsorted_fh.tell()\n- line = unsorted_fh.readline()\n- if not line:\n- break\n- if line.startswith( ">" ):\n- line = line.split( None, 1 )[0][1:]\n- fasta_offsets[ line ] = offset\n- unsorted_fh.close()\n- current_order = map( lambda x: x[1], sorted( map( lambda x: ( x[1], x[0] ), fasta_offsets.items() ) ) )\n- return ( unsorted_filename, fasta_offsets, current_order )\n-\n-\n-def _write_sorted_fasta( sorted_names, fasta_offsets, sorted_fasta_filename, unsorted_fasta_filename ):\n- unsorted_fh = open( unsorted_fasta_filename )\n- sorted_fh'..b'fh.read( CHUNK_SIZE )\n- if data:\n- fasta_writer.write( data )\n- last_char = data[-1]\n- else:\n- break\n- if close_stream:\n- fh.close()\n- else:\n- while True:\n- data = fasta_stream.read( CHUNK_SIZE )\n- if data:\n- fasta_writer.write( data )\n- else:\n- break\n- if close_stream:\n- fasta_stream.close()\n-\n- #sort_fasta( fasta_filename, params[\'param_dict\'][\'sorting\'][\'sort_selector\'], params )\n- \n- \n- return [ ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]\n-\n-\n-def compute_fasta_length( fasta_file, out_file, keep_first_word=False ):\n-\n- infile = fasta_file\n- out = open( out_file, \'w\')\n-\n- fasta_title = \'\'\n- seq_len = 0\n-\n- first_entry = True\n-\n- for line in open( infile ):\n- line = line.strip()\n- if not line or line.startswith( \'#\' ):\n- continue\n- if line[0] == \'>\':\n- if first_entry == False:\n- if keep_first_word:\n- fasta_title = fasta_title.split()[0]\n- out.write( "%s\\t%d\\n" % ( fasta_title[ 1: ], seq_len ) )\n- else:\n- first_entry = False\n- fasta_title = line\n- seq_len = 0\n- else:\n- seq_len += len(line)\n-\n- # last fasta-entry\n- if keep_first_word:\n- fasta_title = fasta_title.split()[0]\n- out.write( "%s\\t%d\\n" % ( fasta_title[ 1: ], seq_len ) )\n- out.close()\n-\n-\n-def _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ):\n- fasta_base_filename = "%s.fa" % sequence_id\n- fasta_filename = os.path.join( target_directory, fasta_base_filename )\n- os.symlink( input_filename, fasta_filename )\n- return [ ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]\n-\n-\n-REFERENCE_SOURCE_TO_DOWNLOAD = dict( ucsc=download_from_ucsc, ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory )\n-\n-SORTING_METHODS = dict( as_is=_sort_fasta_as_is, lexicographical=_sort_fasta_lexicographical, gatk=_sort_fasta_gatk, custom=_sort_fasta_custom )\n-\n-\n-def main():\n- #Parse Command Line\n- parser = optparse.OptionParser()\n- parser.add_option( \'-d\', \'--dbkey_description\', dest=\'dbkey_description\', action=\'store\', type="string", default=None, help=\'dbkey_description\' )\n- parser.add_option( \'-t\', \'--type\', dest=\'file_type\', action=\'store\', type=\'string\', default=None, help=\'file_type\')\n- (options, args) = parser.parse_args()\n- \n- filename = args[0]\n- global DATA_TABLE_NAME\n- if options.file_type == \'representative\':\n- DATA_TABLE_NAME= \'representative_gff\'\n- params = loads( open( filename ).read() )\n- target_directory = params[ \'output_data\' ][0][\'extra_files_path\']\n- os.mkdir( target_directory )\n- data_manager_dict = {}\n- \n- dbkey, dbkey_name, sequence_id, sequence_name = get_dbkey_dbname_id_name( params, dbkey_description=options.dbkey_description ) \n- \n- if dbkey in [ None, \'\', \'?\' ]:\n- raise Exception( \'"%s" is not a valid dbkey. You must specify a valid dbkey.\' % ( dbkey ) )\n-\n- # Create a tmp_dir, in case a zip file needs to be uncompressed\n- tmp_dir = tempfile.mkdtemp()\n- #Fetch the FASTA\n- try:\n- REFERENCE_SOURCE_TO_DOWNLOAD[ params[\'param_dict\'][\'reference_source\'][\'reference_source_selector\'] ]( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir )\n- finally:\n- cleanup_before_exit(tmp_dir)\n- #save info to json file\n- open( filename, \'wb\' ).write( dumps( data_manager_dict ).encode() )\n- \n-if __name__ == "__main__":\n- main()\n' |
| b |
| diff -r 6cd60ba8a842 -r c5dea2080109 data_manager/data_manager_fetch_gff.xml --- a/data_manager/data_manager_fetch_gff.xml Tue Aug 14 11:14:52 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,66 +0,0 @@ -<tool id="data_manager_fetch_gff" name="Create entries in gff data table" version="0.0.1" tool_type="manage_data"> - <description>fetching</description> - <command><![CDATA[ - python "$__tool_directory__"/data_manager_fetch_gff.py "${out_file}" - --type $file_type - --dbkey_description ${ dbkey.get_display_text() } - - ]]></command> - <inputs> - <param name="file_type" type="select" label="GFF file with only one representative transcript per gene (for htseq-count use) or full features file"> - <option value="representative">Representative GFF</option> - <option value="full">GFF with complete features</option> - </param> - - <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> - <param type="text" name="sequence_name" value="" label="Name of sequence" /> - <param type="text" name="sequence_id" value="" label="ID for sequence" /> - <conditional name="reference_source"> - <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> - <option value="url">URL</option> - <option value="history">History</option> - <option value="directory">Directory on Server</option> - </param> - <when value="url"> - <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" /> - </when> - <when value="history"> - <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" /> - </when> - <when value="directory"> - <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" /> - <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" checked="False" /> - </when> - </conditional> - </inputs> - <outputs> - <data name="out_file" format="data_manager_json"/> - </outputs> - <tests> - <!-- TODO: need some way to test that new entry was added to data table --> - <test> - <param name="dbkey" value="anoGam1"/> - <param name="sequence_name" value=""/> - <param name="sequence_desc" value=""/> - <param name="sequence_id" value=""/> - <param name="reference_source_selector" value="history"/> - <param name="input_fasta" value="phiX174.fasta"/> - <param name="sort_selector" value="as_is"/> - <output name="out_file" file="phiX174.data_manager_json"/> - </test> - </tests> - <help> -**What it does** - -Fetches a gff file from various sources (URL, Galaxy History, or a server directory) and populates the "all_gff" data table. - ------- - - - -.. class:: infomark - -**Notice:** If you leave name, description, or id blank, it will be generated automatically. - - </help> -</tool> |
| b |
| diff -r 6cd60ba8a842 -r c5dea2080109 data_manager/salmon_index_builder.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/salmon_index_builder.py Tue Aug 14 11:19:49 2018 -0400 |
| [ |
| @@ -0,0 +1,82 @@ +#!/usr/bin/env python +# Based heavily on the kallisto data manager wrapper script by iuc +from __future__ import print_function + +import argparse +import os +import subprocess +import sys +from json import dumps, loads + +DEFAULT_DATA_TABLE_NAME = "salmon_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_salmon_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 ) + if options.kmer_size != '': + args.append('-k') + args.append(options.kmer_size) + args.extend( [ '-t' , options.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='salmon_indexes' ) + parser.add_argument( '-k', '--kmer_size', dest='kmer_size', action='store', type=str, help='kmer_size' ) + 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_salmon_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() |
| b |
| diff -r 6cd60ba8a842 -r c5dea2080109 data_manager/salmon_index_builder.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/salmon_index_builder.xml Tue Aug 14 11:19:49 2018 -0400 |
| [ |
| @@ -0,0 +1,38 @@ +<tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="0.9.1"> + <description>index builder</description> + <requirements> + <requirement type="package" version="0.9.1">salmon</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/salmon_index_builder.py' --output '${out_file}' + --fasta_filename '${all_fasta_source.fields.path}' + --fasta_dbkey '${all_fasta_source.fields.dbkey}' + --fasta_description '${all_fasta_source.fields.name}' + --kmer_size "${kmer_size}" + --data_table_name salmon_indexes + ]]> + </command> + <inputs> + <param label="Source FASTA Sequence" name="all_fasta_source" type="select"> + <options from_data_table="all_fasta" /> + </param> + <param name="sequence_name" type="text" value="" label="Name of sequence" /> + <param name="sequence_id" type="text" value="" label="ID for sequence" /> + <param name="kmer_size" type="integer" optional='true' value="21" max="32" label="The size of the k-mer on which the index is built" + help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers, the more distinct they will be. We generally recommend using a k-mer size of at least 20. MUST BE AN ODD VALUE "/> + + + + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <help> +<![CDATA[ +.. class:: infomark + +**Notice:** If you leave name, description, or id blank, it will be generated automatically. +]]> + </help> +</tool> + |
| b |
| diff -r 6cd60ba8a842 -r c5dea2080109 data_manager_conf.xml --- a/data_manager_conf.xml Tue Aug 14 11:14:52 2018 -0400 +++ b/data_manager_conf.xml Tue Aug 14 11:19:49 2018 -0400 |
| b |
| @@ -1,32 +1,17 @@ <?xml version="1.0"?> <data_managers> -<data_manager tool_file="data_manager/data_manager_fetch_gff.xml" id="data_manager_fetch_gff"> - <data_table name="all_gff"> + <data_manager tool_file="data_manager/salmon_index_builder.xml" id="salmon_index_builder" version="0.1"> + <data_table name="salmon_indexes"> <output> <column name="value" /> <column name="dbkey" /> <column name="name" /> - <column name="path" output_ref="out_file"> - <move type="file"> - <source>${path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/gff/${path}</target> + <column name="path" output_ref="out_file" > + <move type="directory" relativize_symlinks="True"> + <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base --> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/salmon_index/${value}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/gff/${path}</value_translation> - <value_translation type="function">abspath</value_translation> - </column> - </output> - </data_table> - <data_table name="representative_gff"> - <output> - <column name="value" /> - <column name="dbkey" /> - <column name="name" /> - <column name="path" output_ref="out_file"> - <move type="file"> - <source>${path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/representative_gff/${path}</target> - </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/representative_gff/${path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/salmon_index/${value}/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output> |
| b |
| diff -r 6cd60ba8a842 -r c5dea2080109 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 14 11:19:49 2018 -0400 |
| b |
| @@ -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): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#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. +# |
| b |
| diff -r 6cd60ba8a842 -r c5dea2080109 tool-data/all_gff.loc.sample --- a/tool-data/all_gff.loc.sample Tue Aug 14 11:14:52 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -#The all_gff.loc file has this format: -# -#<unique_build_id> <dbkey> <display_name> <path_to_gff_file> |
| b |
| diff -r 6cd60ba8a842 -r c5dea2080109 tool-data/representative_gff.loc.sample --- a/tool-data/representative_gff.loc.sample Tue Aug 14 11:14:52 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -#The representative_gff.loc file has this format: -# -#<unique_build_id> <dbkey> <display_name> <path_to_gff_file> |
| b |
| diff -r 6cd60ba8a842 -r c5dea2080109 tool-data/salmon_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/salmon_indexes.loc.sample Tue Aug 14 11:19:49 2018 -0400 |
| b |
| @@ -0,0 +1,28 @@ +# salmon_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 Salmon. +# 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. +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +# So, for example, if you had sacCer3 indexes stored in: +# +# /depot/data2/galaxy/sacCer3/salmon_indexes/ +# +# then the salmon_indexes.loc entry could look like this: +# +#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/salmon_indexes +# +#More examples: +# +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/salmon_indexes/mm10 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/salmon_indexes/dm3 +# +# |
| b |
| diff -r 6cd60ba8a842 -r c5dea2080109 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Tue Aug 14 11:14:52 2018 -0400 +++ b/tool_data_table_conf.xml.sample Tue Aug 14 11:19:49 2018 -0400 |
| b |
| @@ -1,5 +1,12 @@ -<?xml version="1.0"?> <tables> - <table name="all_gff" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/all_gff.loc" /> </table> - <table name="representative_gff" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/representative_gff.loc" /> </table> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> + <!-- Locations of indexes in the kallisto mapper format --> + <table name="salmon_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/salmon_indexes.loc" /> + </table> </tables> |