| Previous changeset 0:ce62d0912b10 (2015-02-08) Next changeset 2:5558f74bd296 (2021-03-21) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4" |
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modified:
data_manager/data_manager_diamond_database_builder.py data_manager/data_manager_diamond_database_builder.xml |
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added:
test-data/diamond_data_manager.json test-data/diamond_database.loc test-data/phiX174.fasta tool_data_table_conf.xml.test |
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removed:
.shed.yml tool_dependencies.xml |
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| diff -r ce62d0912b10 -r 5a0d0bee4f8d .shed.yml --- a/.shed.yml Sun Feb 08 10:05:20 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -owner: bgruening -name: data_manager_diamond_database_builder |
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| diff -r ce62d0912b10 -r 5a0d0bee4f8d data_manager/data_manager_diamond_database_builder.py --- a/data_manager/data_manager_diamond_database_builder.py Sun Feb 08 10:05:20 2015 -0500 +++ b/data_manager/data_manager_diamond_database_builder.py Tue Dec 03 17:39:48 2019 -0500 |
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| b'@@ -1,4 +1,5 @@\n #!/usr/bin/env python\n+import json\n import sys\n import os\n import tempfile\n@@ -12,13 +13,12 @@\n import gzip\n import bz2\n \n-from galaxy.util.json import from_json_string, to_json_string\n+CHUNK_SIZE = 2**20 # 1mb\n \n-CHUNK_SIZE = 2**20 #1mb\n \n-def cleanup_before_exit( tmp_dir ):\n- if tmp_dir and os.path.exists( tmp_dir ):\n- shutil.rmtree( tmp_dir )\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@@ -26,146 +26,146 @@\n sys.exit(1)\n \n \n-def _get_files_in_ftp_path( ftp, path ):\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+ 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( file_obj, tmp_dir ):\n- fasta_tar = tarfile.open( fileobj=file_obj, mode=\'r:*\' )\n- return [ fasta_tar.extractfile( member ) for member in fasta_tar.getmembers() ]\n+def _get_stream_readers_for_tar(file_obj, tmp_dir):\n+ fasta_tar = tarfile.open(fileobj=file_obj, mode=\'r:*\')\n+ return [fasta_tar.extractfile(member) for member in fasta_tar.getmembers()]\n \n \n-def _get_stream_readers_for_zip( file_obj, tmp_dir ):\n- fasta_zip = zipfile.ZipFile( file_obj, \'r\' )\n+def _get_stream_readers_for_zip(file_obj, tmp_dir):\n+ fasta_zip = zipfile.ZipFile(file_obj, \'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+ 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( file_obj, tmp_dir ):\n- return [ gzip.GzipFile( fileobj=file_obj, mode=\'rb\' ) ]\n+def _get_stream_readers_for_gzip(file_obj, tmp_dir):\n+ return [gzip.GzipFile(fileobj=file_obj, mode=\'rb\')]\n \n \n-def _get_stream_readers_for_bz2( file_obj, tmp_dir ):\n- return [ bz2.BZ2File( file_obj.name, \'rb\' ) ]\n+def _get_stream_readers_for_bz2(file_obj, tmp_dir):\n+ return [bz2.BZ2File(file_obj.name, \'rb\')]\n \n \n-def download_from_ncbi( data_manager_dict, params, target_directory, database_id, database_name ):\n+def download_from_ncbi(data_manager_dict, params, target_directory, database_id, database_name):\n NCBI_FTP_SERVER = \'ftp.ncbi.nlm.nih.gov\'\n NCBI_DOWNLOAD_PATH = \'/blast/db/FASTA/\'\n- COMPRESSED_EXTENSIONS = [ ( \'.tar.gz\', _get_stream_readers_for_tar ), ( \'.tar.bz2\', _get_stream_readers_for_tar ), ( \'.zip\', _get_stream_readers_for_zip ), ( \'.gz\', _get_stream_readers_for_gzip ), ( \'.bz2\', _get_stream_readers_for_bz2 ) ]\n+ COMPRESSED_EXTENSIONS = [(\'.tar.gz\', _get_stream_readers_for_tar), (\'.tar.bz2\', _get_stream_readers_for_tar), (\'.zip\', _get_stream_readers_for_zip), (\'.gz\', _get_stream_readers_for_gzip), (\'.bz2\', _get_stream_readers_for_bz2)]\n \n ncbi_identifier = params[\'param_dict\'][\'reference_source\'][\'requested_identifier\']\n- ftp = FTP( NCBI_FTP_SERVER )\n+ ftp = FTP(NCBI_FTP_SERVER)\n ftp.login()\n \n- path_contents = _get_files_in_ftp_path( ftp, NCBI_DOWNLOAD_PATH )\n+ path_contents = _get_files_in_ftp_path(ftp, NCBI_DOWNLOAD_PATH)\n \n ncbi_file_name = None\n get_stream_reader = None\n ext = None\n for ext, get_stream_reader in COMPRESSED_EXTENSIONS:\n- if "%s%s" % ( ncbi_identifier, ext ) in path_contents:\n- ncbi_file_name = "%s%s%s" % ( NCBI_DOWNLOAD_PATH, ncbi_identifier, ext )\n+ if "%s%s" % (ncbi_identifier, ext) in path_contents:\n+ ncbi_file_name = "%s%s%s" % (NCBI_DOWNLOAD_PATH, ncbi_identifier, ext)\n break\n \n if not ncbi_file_name:\n- raise Exception( \'Unable to determine filename for NCBI database for %s: %s\' % ( ncbi_identifier, path_contents ) )\n+ raise Exception(\'Unable'..b'ak\n if close_stream:\n@@ -183,56 +183,58 @@\n \n fasta_writer.close()\n \n- args = [ \'diamond\', \'makedb\', \'--in\', temp_fasta.name, \'--db\', fasta_filename]\n+ args = [\'diamond\', \'makedb\', \'--in\', temp_fasta.name, \'--db\', fasta_filename]\n \n- tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-diamond-database-builder-stderr" )\n- proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )\n+ tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-diamond-database-builder-stderr")\n+ proc = subprocess.Popen(args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno())\n return_code = proc.wait()\n if return_code:\n tmp_stderr.flush()\n tmp_stderr.seek(0)\n print >> sys.stderr, "Error building diamond database:"\n while True:\n- chunk = tmp_stderr.read( CHUNK_SIZE )\n+ chunk = tmp_stderr.read(CHUNK_SIZE)\n if not chunk:\n break\n- sys.stderr.write( chunk )\n- sys.exit( return_code )\n+ sys.stderr.write(chunk)\n+ sys.exit(return_code)\n tmp_stderr.close()\n- os.remove( temp_fasta.name )\n- return dict( value=database_id, name=database_name, db_path="%s.dmnd" % fasta_base_filename )\n+ os.remove(temp_fasta.name)\n+ return dict(value=database_id, name=database_name, db_path="%s.dmnd" % fasta_base_filename)\n \n \n-def _create_symlink( input_filename, target_directory, database_id, database_name ):\n+def _create_symlink(input_filename, target_directory, database_id, database_name):\n fasta_base_filename = "%s.fa" % database_id\n- fasta_filename = os.path.join( target_directory, fasta_base_filename )\n- os.symlink( input_filename, fasta_filename )\n- return dict( value=database_id, name=database_name, db_path=fasta_base_filename )\n+ fasta_filename = os.path.join(target_directory, fasta_base_filename)\n+ os.symlink(input_filename, fasta_filename)\n+ return dict(value=database_id, name=database_name, db_path=fasta_base_filename)\n \n \n-REFERENCE_SOURCE_TO_DOWNLOAD = dict( ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory )\n+REFERENCE_SOURCE_TO_DOWNLOAD = dict(ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory)\n+\n \n def main():\n- #Parse Command Line\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(\'-d\', \'--dbkey_description\', dest=\'dbkey_description\', action=\'store\', type="string", default=None, help=\'dbkey_description\')\n (options, args) = parser.parse_args()\n- \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+\n+ params = json.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 database_id = params[\'param_dict\'][\'database_id\']\n database_name = params[\'param_dict\'][\'database_name\']\n \n- #Fetch the FASTA\n- REFERENCE_SOURCE_TO_DOWNLOAD[ params[\'param_dict\'][\'reference_source\'][\'reference_source_selector\'] ]( data_manager_dict, params, target_directory, database_id, database_name )\n- \n- #save info to json file\n- open( filename, \'wb\' ).write( to_json_string( data_manager_dict ) )\n+ # Fetch the FASTA\n+ REFERENCE_SOURCE_TO_DOWNLOAD[params[\'param_dict\'][\'reference_source\'][\'reference_source_selector\']](data_manager_dict, params, target_directory, database_id, database_name)\n+\n+ # save info to json file\n+ open(filename, \'w\').write(json.dumps(data_manager_dict, sort_keys=True))\n+\n \n if __name__ == "__main__":\n main()\n' |
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| diff -r ce62d0912b10 -r 5a0d0bee4f8d data_manager/data_manager_diamond_database_builder.xml --- a/data_manager/data_manager_diamond_database_builder.xml Sun Feb 08 10:05:20 2015 -0500 +++ b/data_manager/data_manager_diamond_database_builder.xml Tue Dec 03 17:39:48 2019 -0500 |
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| @@ -1,10 +1,11 @@ -<tool id="diamond_database_builder" name="Diamond" tool_type="manage_data" version="0.0.1"> +<tool id="diamond_database_builder" name="Diamond" tool_type="manage_data" version="0.0.2"> <description> Database builder</description> <requirements> - <requirement type="package" version="0.6.13">diamond</requirement> + <requirement type="package" version="0.9.29">diamond</requirement> + <requirement type="package" version="2.7">python</requirement> </requirements> - <command interpreter="python"> - data_manager_diamond_database_builder.py "${out_file}" + <command> + python '$__tool_directory__/data_manager_diamond_database_builder.py' '${out_file}' </command> <inputs> <param type="text" name="database_name" value="" label="Database name or description" @@ -35,6 +36,17 @@ <outputs> <data name="out_file" format="data_manager_json"/> </outputs> + <tests> + <test> + <param name="database_name" value="PhiX174"/> + <param name="database_id" value="sequence_id"/> + <conditional name="reference_source"> + <param name="reference_source_selector" value="history"/> + <param name="input_fasta" value="phiX174.fasta"/> + </conditional> + <output name="out_file" value="diamond_data_manager.json"/> + </test> + </tests> <help> .. class:: infomark @@ -43,4 +55,7 @@ For example the NR database can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz </help> + <citations> + <citation type="doi">10.1038/nmeth.3176</citation> + </citations> </tool> |
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| diff -r ce62d0912b10 -r 5a0d0bee4f8d test-data/diamond_data_manager.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_data_manager.json Tue Dec 03 17:39:48 2019 -0500 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"diamond_database": [{"db_path": "sequence_id.fa.dmnd", "name": "PhiX174", "value": "sequence_id"}]}} \ No newline at end of file |
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| diff -r ce62d0912b10 -r 5a0d0bee4f8d test-data/diamond_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_database.loc Tue Dec 03 17:39:48 2019 -0500 |
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| @@ -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. +# |
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| diff -r ce62d0912b10 -r 5a0d0bee4f8d test-data/phiX174.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX174.fasta Tue Dec 03 17:39:48 2019 -0500 |
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| @@ -0,0 +1,79 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA + |
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| diff -r ce62d0912b10 -r 5a0d0bee4f8d tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Dec 03 17:39:48 2019 -0500 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files required to build Diamond databases --> + <table name="diamond_database" comment_char="#"> + <columns>value, name, db_path</columns> + <file path="${__HERE__}/test-data/diamond_database.loc" /> + </table> +</tables> |
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| diff -r ce62d0912b10 -r 5a0d0bee4f8d tool_dependencies.xml --- a/tool_dependencies.xml Sun Feb 08 10:05:20 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="diamond" version="0.6.13"> - <repository changeset_revision="47c4dfd5aed5" name="package_diamond_0_6_13" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |