| Next changeset 1:85a23e2dd92b (2016-06-07) |
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Commit message:
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added:
data_manager/data_manager_snpEff_databases.py data_manager/data_manager_snpEff_databases.xml data_manager/data_manager_snpEff_download.py data_manager/data_manager_snpEff_download.xml data_manager_conf.xml repository_dependencies.xml tool-data/snpeffv_annotations.loc.sample tool-data/snpeffv_databases.loc.sample tool-data/snpeffv_genomedb.loc.sample tool-data/snpeffv_regulationdb.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 000000000000 -r 9ac823a8b328 data_manager/data_manager_snpEff_databases.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_snpEff_databases.py Thu Jan 22 09:14:50 2015 -0500 |
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| @@ -0,0 +1,82 @@ +#!/usr/bin/env python + +import sys +import os +import re +import tempfile +import subprocess +import fileinput +import shutil +import optparse +import urllib2 +from ftplib import FTP +import tarfile + +from galaxy.util.json import from_json_string, to_json_string + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit(1) + +def fetch_databases(data_manager_dict, target_directory, jar_path): + (snpEff_dir,snpEff_jar) = os.path.split(jar_path) + if not os.path.exists(target_directory): + os.makedirs(target_directory) + databases_path = os.path.join( target_directory, 'databases.out' ) + databases_output = open(databases_path,'w') + args = [ 'java','-jar', ] + args.append( snpEff_jar ) + args.append( 'databases' ) + # tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-snpEff-stderr" ) + # databases_output = open(databases_path) + # proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno(), stderr=tmp_stderr.fileno() ) + proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno() ) + return_code = proc.wait() + if return_code: + sys.exit( return_code ) + databases_output.close() + try: + data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) + data_manager_dict['data_tables']['snpeff4_databases'] = data_manager_dict['data_tables'].get( 'snpeff4_databases', [] ) + data_table_entries = [] + fh = open(databases_path,'r') + for i,line in enumerate(fh): + fields = line.split('\t') + if len(fields) >= 2: + genome_version = fields[0].strip() + if genome_version.startswith("Genome") or genome_version.startswith("-"): + continue + #snpeff test genome + if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'): + continue + description = fields[1].strip() + ' : ' + genome_version + data_table_entries.append(dict(value=genome_version, name=description)) + data_manager_dict['data_tables']['snpeff4_databases'] = data_table_entries + except Exception, e: + stop_err( 'Error parsing %s %s\n' % (config,str( e )) ) + else: + fh.close() + return data_manager_dict + +def main(): + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option( '-j', '--jar_path', dest='jar_path', action='store', type="string", default=None, help='snpEff.jar path' ) + (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 = {} + + + #Create Defuse Reference Data + data_manager_dict = fetch_databases( data_manager_dict, target_directory, options.jar_path) + + #save info to json file + open( filename, 'wb' ).write( to_json_string( data_manager_dict ) ) + +if __name__ == "__main__": main() + |
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| diff -r 000000000000 -r 9ac823a8b328 data_manager/data_manager_snpEff_databases.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_snpEff_databases.xml Thu Jan 22 09:14:50 2015 -0500 |
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| @@ -0,0 +1,41 @@ +<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.0.0" tool_type="manage_data"> + <description>Read the list of available snpEff databases</description> + <requirements> + <requirement type="package" version="4.0">snpEff</requirement> + </requirements> + <command interpreter="python"> + data_manager_snpEff_databases.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar "$out_file" + </command> + <inputs> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <tests> + <test> + <output name="out_file"> + <assert_contents> + <!-- Check that a genome was added --> + <has_text text="GRCh38.76" /> + </assert_contents> + </output> + </test> + </tests> + <help> + +This tool updatess the list of SnpEff databases for the SnpEff Download data manager. +It should only need to be run once for a snpEff version, +since it populates the SnpEff Download data manager from the snpEff config file. + +For information about snpEff: http://snpEff.sourceforge.net + +Please cite: +"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] + + </help> +</tool> + |
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| diff -r 000000000000 -r 9ac823a8b328 data_manager/data_manager_snpEff_download.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_snpEff_download.py Thu Jan 22 09:14:50 2015 -0500 |
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| b'@@ -0,0 +1,205 @@\n+#!/usr/bin/env python\n+\n+import sys\n+import os\n+import re\n+import tempfile\n+import subprocess\n+import fileinput\n+import shutil\n+import optparse\n+import urllib2\n+import gzip\n+from ftplib import FTP\n+import tarfile\n+\n+from galaxy.util.json import from_json_string, to_json_string\n+\n+def stop_err(msg):\n+ sys.stderr.write(msg)\n+ sys.exit(1)\n+\n+\n+def fetch_databases(jar_path,genome_list=None):\n+ snpDBs = dict()\n+ (snpEff_dir,snpEff_jar) = os.path.split(jar_path)\n+ databases_path = \'databases.out\' \n+ databases_output = open(databases_path,\'w\')\n+ args = [ \'java\',\'-jar\', ]\n+ args.append( snpEff_jar )\n+ args.append( \'databases\' )\n+ # tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-snpEff-stderr" )\n+ # databases_output = open(databases_path)\n+ # proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno(), stderr=tmp_stderr.fileno() )\n+ proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno() )\n+ return_code = proc.wait()\n+ if return_code:\n+ sys.exit( return_code )\n+ databases_output.close()\n+ try:\n+ fh = open(databases_path,\'r\')\n+ for i,line in enumerate(fh):\n+ fields = line.split(\'\\t\')\n+ if len(fields) >= 2:\n+ genome_version = fields[0].strip()\n+ if genome_list and genome_version not in genome_list:\n+ continue\n+ if genome_version.startswith("Genome") or genome_version.startswith("-"):\n+ continue\n+ description = fields[1].strip()\n+ snpDBs[genome_version] = description;\n+ except Exception, e:\n+ stop_err( \'Error parsing %s %s\\n\' % (config,str( e )) )\n+ else:\n+ fh.close()\n+ return snpDBs\n+\n+def getOrganismNames(jar_path,genomes,organisms) :\n+ genome_list = genomes.split(\',\')\n+ organism_list = organisms.split(\',\') if organisms else []\n+ if len(genome_list) != len(organism_list):\n+ descriptions = []\n+ snpDBdict = fetch_databases(jar_path,genome_list=genome_list); \n+ for genome in snpDBdict:\n+ descriptions.append(snpDBdict[genome] if genome in snpDBdict else genome)\n+ return \',\'.join(descriptions)\n+ return organisms \n+\n+def getSnpeffVersion(jar_path):\n+ snpeff_version = \'SnpEff ?.?\'\n+ (snpEff_dir,snpEff_jar) = os.path.split(jar_path)\n+ stderr_path = \'snpeff.err\'\n+ stderr_fh = open(stderr_path,\'w\')\n+ args = [ \'java\',\'-jar\', ]\n+ args.append( snpEff_jar )\n+ args.append( \'-h\' )\n+ proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stderr=stderr_fh.fileno() )\n+ return_code = proc.wait()\n+ if return_code != 255:\n+ sys.exit( return_code )\n+ stderr_fh.close()\n+ fh = open(stderr_path,\'r\')\n+ for line in fh:\n+ m = re.match(\'^[Ss]npEff version (SnpEff)\\s*(\\d+\\.\\d+).*$\',line)\n+ if m:\n+ snpeff_version = m.groups()[0] + m.groups()[1]\n+ break\n+ fh.close()\n+ return snpeff_version\n+\n+# Starting with SnpEff 4.1 the .bin files contain the SnpEff version:\n+# Example - the first 3 line of GRCh37.75/snpEffectPredictor.bin (uncompressed):\n+"""\n+SnpEff 4.1\n+CHROMOSOME 2 1 0 179197 GL000219.1 false\n+CHROMOSOME 3 1 0 81347269 HSCHR17_1 false\n+"""\n+def getSnpeffVersionFromFile(path):\n+ snpeff_version = None\n+ try:\n+ fh = gzip.open(path, \'rb\')\n+ buf = fh.read(100)\n+ lines = buf.splitlines()\n+ m = re.match(\'^(SnpEff)\\s+(\\d+\\.\\d+).*$\',lines[0].strip())\n+ if m:\n+ snpeff_version = m.groups()[0] + m.groups()[1]\n+ fh.close()\n+ except Exception, e:\n+ stop_err( \'Error parsing SnpEff version from: %s %s\\n\' % (path,str( e )) )\n+ return snpeff_version \n+\n+"""\n+# Download human database \'hg19\'\n+java -jar snpEff.jar download -v hg19\n+\n+ <command'..b'\n+ args = [ \'java\',\'-jar\' ]\n+ args.append( jar_path )\n+ args.append( \'download\' )\n+ args.append( \'-c\' )\n+ args.append( config )\n+ args.append( \'-dataDir\' )\n+ args.append( data_dir )\n+ args.append( \'-v\' )\n+ args.append( genome_version )\n+ proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir )\n+ return_code = proc.wait()\n+ if return_code:\n+ sys.exit( return_code )\n+ ## search data_dir/genome_version for files\n+ regulation_pattern = \'regulation_(.+).bin\'\n+ # annotation files that are included in snpEff by a flag\n+ annotations_dict = {\'nextProt.bin\' : \'-nextprot\',\'motif.bin\': \'-motif\'}\n+ genome_path = os.path.join(data_dir,genome_version)\n+ snpeff_version = getSnpeffVersion(jar_path)\n+ key = snpeff_version + \'_\' + genome_version \n+ if os.path.isdir(genome_path):\n+ for root, dirs, files in os.walk(genome_path):\n+ for fname in files:\n+ if fname.startswith(\'snpEffectPredictor\'):\n+ # if snpEffectPredictor.bin download succeeded\n+ name = genome_version + (\' : \' + organism if organism else \'\') \n+ # version = getSnpeffVersionFromFile(os.path.join(root,fname))\n+ data_table_entry = dict(key=key,version=snpeff_version,value=genome_version, name=name, path=data_dir)\n+ _add_data_table_entry( data_manager_dict, \'snpeffv_genomedb\', data_table_entry )\n+ else:\n+ m = re.match(regulation_pattern,fname)\n+ if m:\n+ name = m.groups()[0]\n+ data_table_entry = dict(key=key,version=snpeff_version,genome=genome_version,value=name, name=name)\n+ _add_data_table_entry( data_manager_dict, \'snpeffv_regulationdb\', data_table_entry )\n+ elif fname in annotations_dict:\n+ value = annotations_dict[fname]\n+ name = value.lstrip(\'-\')\n+ data_table_entry = dict(key=key,version=snpeff_version,genome=genome_version,value=value, name=name)\n+ _add_data_table_entry( data_manager_dict, \'snpeffv_annotations\', data_table_entry )\n+ return data_manager_dict\n+\n+def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ):\n+ data_manager_dict[\'data_tables\'] = data_manager_dict.get( \'data_tables\', {} )\n+ data_manager_dict[\'data_tables\'][data_table] = data_manager_dict[\'data_tables\'].get( data_table, [] )\n+ data_manager_dict[\'data_tables\'][data_table].append( data_table_entry )\n+ return data_manager_dict\n+\n+def main():\n+ #Parse Command Line\n+ parser = optparse.OptionParser()\n+ parser.add_option( \'-j\', \'--jar_path\', dest=\'jar_path\', action=\'store\', type="string", default=None, help=\'snpEff.jar path\' )\n+ parser.add_option( \'-c\', \'--config\', dest=\'config\', action=\'store\', type="string", default=None, help=\'snpEff.config path\' )\n+ parser.add_option( \'-g\', \'--genome_version\', dest=\'genome_version\', action=\'store\', type="string", default=None, help=\'genome_version\' )\n+ parser.add_option( \'-o\', \'--organism\', dest=\'organism\', action=\'store\', type="string", default=None, help=\'organism name\' )\n+ (options, args) = parser.parse_args()\n+\n+ filename = args[0]\n+\n+ params = from_json_string( open( filename ).read() )\n+ target_directory = params[ \'output_data\' ][0][\'extra_files_path\']\n+ os.mkdir( target_directory )\n+ data_manager_dict = {}\n+\n+\n+ #Create SnpEff Reference Data\n+ for genome_version, organism in zip(options.genome_version.split(\',\'), getOrganismNames(options.jar_path,options.genome_version,options.organism).split(\',\')):\n+ download_database( data_manager_dict, target_directory, options.jar_path, options.config, genome_version, organism )\n+\n+ #save info to json file\n+ open( filename, \'wb\' ).write( to_json_string( data_manager_dict ) )\n+\n+if __name__ == "__main__": main()\n+\n' |
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| diff -r 000000000000 -r 9ac823a8b328 data_manager/data_manager_snpEff_download.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_snpEff_download.xml Thu Jan 22 09:14:50 2015 -0500 |
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| @@ -0,0 +1,53 @@ +<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.0.0" tool_type="manage_data"> + <description>Download a new database</description> + <requirements> + <requirement type="package" version="4.0">snpEff</requirement> + </requirements> + <command interpreter="python"> + data_manager_snpEff_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config + --genome_version "$genome_version" "$out_file" + </command> + <inputs> + <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> + <help>https://snpeff-data.galaxyproject.org/databases/</help> + <validator type="regex" message="A genome version name is required">\S+</validator> + </param> + </inputs> + + <outputs> + <data name="out_file" format="data_manager_json" label="${tool.name}"/> + </outputs> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <tests> + <test> + <param name="genome_version" value="GRCh38.76"/> + <output name="out_file"> + <assert_contents> + <!-- Check that a genome was added --> + <has_text text="GRCh38.76" /> + <has_text text="snpeffv_regulationdb" /> + <has_text text="snpeffv_annotations" /> + </assert_contents> + </output> + </test> + </tests> + <help> + +This tool downloads a SnpEff database and populates data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations. + +To see the list of available SnpEff genomes run the "SnpEff Databases" data manager which records the available genome databases in data table: snpeff4_databases + +The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/ + + +For details about this tool, please go to http://snpEff.sourceforge.net + +Please cite: +"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] + + </help> +</tool> + |
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| diff -r 000000000000 -r 9ac823a8b328 data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Thu Jan 22 09:14:50 2015 -0500 |
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| @@ -0,0 +1,50 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/data_manager_snpEff_databases.xml" id="data_manager_snpeff_databases" > + <data_table name="snpeffv_databases"> <!-- Defines a Data Table to be modified. --> + <output> <!-- Handle the output of the Data Manager Tool --> + <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="version" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> + </output> + </data_table> + </data_manager> + <data_manager tool_file="data_manager/data_manager_snpEff_download.xml" id="data_manager_snpeff_download" > + <data_table name="snpeffv_genomedb"> <!-- Defines a Data Table to be modified. --> + <output> <!-- Handle the output of the Data Manager Tool --> + <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="version" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="path" output_ref="out_file" > + <move type="directory" relativize_symlinks="True"> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">snpEff/v4_0/data</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/snpEff/v4_0/data</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + <data_table name="snpeffv_regulationdb"> <!-- Defines a Data Table to be modified. --> + <output> <!-- Handle the output of the Data Manager Tool --> + <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="version" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="genome" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> + </output> + </data_table> + <data_table name="snpeffv_annotations"> <!-- Defines a Data Table to be modified. --> + <output> <!-- Handle the output of the Data Manager Tool --> + <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="version" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="genome" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> + </output> + </data_table> + </data_manager> +</data_managers> + + |
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| diff -r 000000000000 -r 9ac823a8b328 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Thu Jan 22 09:14:50 2015 -0500 |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="This requires the SnpEff datatype definitions."> + <repository changeset_revision="d78b2b2a3388" name="snpeff_datatypes" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories> |
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| diff -r 000000000000 -r 9ac823a8b328 tool-data/snpeffv_annotations.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/snpeffv_annotations.loc.sample Thu Jan 22 09:14:50 2015 -0500 |
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| @@ -0,0 +1,5 @@ +## Regulation Databases for SnpEff +## These are from the list on: http://snpeff.sourceforge.net/download.html +#key snpeff_version genome annotation_name description +#SnpEff4.0_GRCh37.75 SnpEff4.0 GRCh37.75 nextprot nextprot +#SnpEff4.0_GRCh38.76 SnpEff4.1 GRCh38.76 motif motif |
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| diff -r 000000000000 -r 9ac823a8b328 tool-data/snpeffv_databases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/snpeffv_databases.loc.sample Thu Jan 22 09:14:50 2015 -0500 |
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| @@ -0,0 +1,5 @@ +## Available Databases for SnpEff +## These are from the list on: http://snpeff.sourceforge.net/download.html +## the Description field in this sample is "Genome : Version" +#key snpeff_version Version Description +#SnpEff4.0_GRCh37.75 SnpEff4.0 GRCh37.75 Homo sapiens : GRCh37.75 |
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| diff -r 000000000000 -r 9ac823a8b328 tool-data/snpeffv_genomedb.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/snpeffv_genomedb.loc.sample Thu Jan 22 09:14:50 2015 -0500 |
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| @@ -0,0 +1,6 @@ +## Downloaded Databases for SnpEff +## These are from the list on: http://snpeff.sourceforge.net/download.html +## the Description field in this sample is "Genome : Version" +#Key snpeff_version Version Description data_dir path +#SnpEff4.0_GRCh37.74 SnpEff4.0 GRCh37.74 Homo sapiens : GRCh37.74 /home/galaxy/snpEff/v4_0/data +#SnpEff4.1_GRCh38.76 SnpEff4.1 GRCh38.76 Homo sapiens : GRCh38.76 /home/galaxy/snpEff/v4_1/data |
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| diff -r 000000000000 -r 9ac823a8b328 tool-data/snpeffv_regulationdb.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/snpeffv_regulationdb.loc.sample Thu Jan 22 09:14:50 2015 -0500 |
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| @@ -0,0 +1,5 @@ +## Regulation Databases for SnpEff +## These are from the list on: http://snpeff.sourceforge.net/download.html +#Key snpeff_version genome regulation_name description +#SnpEff4.0_GRCh37.74 SnpEff4.0 GRCh37.74 CD4 CD4 +#SnpEff4.1_GRCh38.76 SnpEff4.1 GRCh38.76 CD4 CD4 |
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| diff -r 000000000000 -r 9ac823a8b328 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Jan 22 09:14:50 2015 -0500 |
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| @@ -0,0 +1,19 @@ +<tables> + <table name="snpeffv_genomedb" comment_char="#"> + <columns>key, version, value, name, path</columns> + <file path="tool-data/snpeffv_genomedb.loc" /> + </table> + <table name="snpeffv_regulationdb" comment_char="#"> + <columns>key, version, genome, value, name</columns> + <file path="tool-data/snpeffv_regulationdb.loc" /> + </table> + <table name="snpeffv_annotations" comment_char="#"> + <columns>key, version, genome, value, name</columns> + <file path="tool-data/snpeffv_annotations.loc" /> + </table> + <table name="snpeffv_databases" comment_char="#"> + <columns>key, version, value, name</columns> + <file path="tool-data/snpeffv_databases.loc" /> + </table> +</tables> + |
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| diff -r 000000000000 -r 9ac823a8b328 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jan 22 09:14:50 2015 -0500 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="snpEff" version="4.0"> + <repository changeset_revision="6bc55957927b" name="package_snpeff_4_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |