Mercurial > repos > bgruening > data_manager_diamond_database_builder

changeset 1:5a0d0bee4f8d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
author bgruening
date Tue, 03 Dec 2019 17:39:48 -0500
parents ce62d0912b10
children 5558f74bd296
files .shed.yml data_manager/data_manager_diamond_database_builder.py data_manager/data_manager_diamond_database_builder.xml test-data/diamond_data_manager.json test-data/diamond_database.loc test-data/phiX174.fasta tool_data_table_conf.xml.test tool_dependencies.xml
diffstat 8 files changed, 236 insertions(+), 122 deletions(-) [+]
line wrap: on
line diff
--- a/.shed.yml	Sun Feb 08 10:05:20 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-owner: bgruening
-name: data_manager_diamond_database_builder
--- 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
@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+import json
 import sys
 import os
 import tempfile
@@ -12,13 +13,12 @@
 import gzip
 import bz2
 
-from galaxy.util.json import from_json_string, to_json_string
+CHUNK_SIZE = 2**20  # 1mb
 
-CHUNK_SIZE = 2**20 #1mb
 
-def cleanup_before_exit( tmp_dir ):
-    if tmp_dir and os.path.exists( tmp_dir ):
-        shutil.rmtree( tmp_dir )
+def cleanup_before_exit(tmp_dir):
+    if tmp_dir and os.path.exists(tmp_dir):
+        shutil.rmtree(tmp_dir)
 
 
 def stop_err(msg):
@@ -26,146 +26,146 @@
     sys.exit(1)
 
 
-def _get_files_in_ftp_path( ftp, path ):
+def _get_files_in_ftp_path(ftp, path):
     path_contents = []
-    ftp.retrlines( 'MLSD %s' % ( path ), path_contents.append )
-    return [ line.split( ';' )[ -1 ].lstrip() for line in path_contents ]
+    ftp.retrlines('MLSD %s' % (path), path_contents.append)
+    return [line.split(';')[-1].lstrip() for line in path_contents]
 
 
-def _get_stream_readers_for_tar( file_obj, tmp_dir ):
-    fasta_tar = tarfile.open( fileobj=file_obj, mode='r:*' )
-    return [ fasta_tar.extractfile( member ) for member in fasta_tar.getmembers() ]
+def _get_stream_readers_for_tar(file_obj, tmp_dir):
+    fasta_tar = tarfile.open(fileobj=file_obj, mode='r:*')
+    return [fasta_tar.extractfile(member) for member in fasta_tar.getmembers()]
 
 
-def _get_stream_readers_for_zip( file_obj, tmp_dir ):
-    fasta_zip = zipfile.ZipFile( file_obj, 'r' )
+def _get_stream_readers_for_zip(file_obj, tmp_dir):
+    fasta_zip = zipfile.ZipFile(file_obj, 'r')
     rval = []
     for member in fasta_zip.namelist():
-        fasta_zip.extract( member, tmp_dir )
-        rval.append( open( os.path.join( tmp_dir, member ), 'rb' ) )
+        fasta_zip.extract(member, tmp_dir)
+        rval.append(open(os.path.join(tmp_dir, member), 'rb'))
     return rval
 
 
-def _get_stream_readers_for_gzip( file_obj, tmp_dir ):
-    return [ gzip.GzipFile( fileobj=file_obj, mode='rb' ) ]
+def _get_stream_readers_for_gzip(file_obj, tmp_dir):
+    return [gzip.GzipFile(fileobj=file_obj, mode='rb')]
 
 
-def _get_stream_readers_for_bz2( file_obj, tmp_dir ):
-    return [ bz2.BZ2File( file_obj.name, 'rb' ) ]
+def _get_stream_readers_for_bz2(file_obj, tmp_dir):
+    return [bz2.BZ2File(file_obj.name, 'rb')]
 
 
-def download_from_ncbi( data_manager_dict, params, target_directory, database_id, database_name ):
+def download_from_ncbi(data_manager_dict, params, target_directory, database_id, database_name):
     NCBI_FTP_SERVER = 'ftp.ncbi.nlm.nih.gov'
     NCBI_DOWNLOAD_PATH = '/blast/db/FASTA/'
-    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 ) ]
+    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)]
 
     ncbi_identifier = params['param_dict']['reference_source']['requested_identifier']
-    ftp = FTP( NCBI_FTP_SERVER )
+    ftp = FTP(NCBI_FTP_SERVER)
     ftp.login()
 
-    path_contents = _get_files_in_ftp_path( ftp, NCBI_DOWNLOAD_PATH )
+    path_contents = _get_files_in_ftp_path(ftp, NCBI_DOWNLOAD_PATH)
 
     ncbi_file_name = None
     get_stream_reader = None
     ext = None
     for ext, get_stream_reader in COMPRESSED_EXTENSIONS:
-        if "%s%s" % ( ncbi_identifier, ext ) in path_contents:
-            ncbi_file_name = "%s%s%s" % ( NCBI_DOWNLOAD_PATH, ncbi_identifier, ext )
+        if "%s%s" % (ncbi_identifier, ext) in path_contents:
+            ncbi_file_name = "%s%s%s" % (NCBI_DOWNLOAD_PATH, ncbi_identifier, ext)
             break
 
     if not ncbi_file_name:
-        raise Exception( 'Unable to determine filename for NCBI database for %s: %s' % ( ncbi_identifier, path_contents ) )
+        raise Exception('Unable to determine filename for NCBI database for %s: %s' % (ncbi_identifier, path_contents))
 
-    tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-ncbi-' )
-    ncbi_fasta_filename = os.path.join( tmp_dir, "%s%s" % ( ncbi_identifier, ext ) )
-    
+    tmp_dir = tempfile.mkdtemp(prefix='tmp-data-manager-ncbi-')
+    ncbi_fasta_filename = os.path.join(tmp_dir, "%s%s" % (ncbi_identifier, ext))
+
     fasta_base_filename = "%s.fa" % database_id
-    fasta_filename = os.path.join( target_directory, fasta_base_filename )
-    fasta_writer = open( fasta_filename, 'wb+' )
-    
-    tmp_extract_dir = os.path.join ( tmp_dir, 'extracted_fasta' )
-    os.mkdir( tmp_extract_dir )
-    
-    tmp_fasta = open( ncbi_fasta_filename, 'wb+' )
-    
-    ftp.retrbinary( 'RETR %s' % ncbi_file_name, tmp_fasta.write )
-    
+    fasta_filename = os.path.join(target_directory, fasta_base_filename)
+    fasta_writer = open(fasta_filename, 'wb+')
+
+    tmp_extract_dir = os.path.join(tmp_dir, 'extracted_fasta')
+    os.mkdir(tmp_extract_dir)
+
+    tmp_fasta = open(ncbi_fasta_filename, 'wb+')
+
+    ftp.retrbinary('RETR %s' % ncbi_file_name, tmp_fasta.write)
+
     tmp_fasta.flush()
-    tmp_fasta.seek( 0 )
-    
-    fasta_readers = get_stream_reader( tmp_fasta, tmp_extract_dir )
-    
-    data_table_entry = _stream_fasta_to_file( fasta_readers, target_directory, database_id, database_name, params )
-    _add_data_table_entry( data_manager_dict, data_table_entry )
-    
+    tmp_fasta.seek(0)
+
+    fasta_readers = get_stream_reader(tmp_fasta, tmp_extract_dir)
+
+    data_table_entry = _stream_fasta_to_file(fasta_readers, target_directory, database_id, database_name, params)
+    _add_data_table_entry(data_manager_dict, data_table_entry)
+
     for fasta_reader in fasta_readers:
         fasta_reader.close()
     tmp_fasta.close()
-    cleanup_before_exit( tmp_dir )
+    cleanup_before_exit(tmp_dir)
 
 
-def download_from_url( data_manager_dict, params, target_directory, database_id, database_name ):
-    #TODO: we should automatically do decompression here
-    urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) )
-    fasta_reader = [ urllib2.urlopen( url ) for url in urls ]
-    
-    data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, database_id, database_name, params )
-    _add_data_table_entry( data_manager_dict, data_table_entry )
+def download_from_url(data_manager_dict, params, target_directory, database_id, database_name):
+    # TODO: we should automatically do decompression here
+    urls = filter(bool, map(lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split('\n')))
+    fasta_reader = [urllib2.urlopen(url) for url in urls]
+
+    data_table_entry = _stream_fasta_to_file(fasta_reader, target_directory, database_id, database_name, params)
+    _add_data_table_entry(data_manager_dict, data_table_entry)
 
 
-def download_from_history( data_manager_dict, params, target_directory, database_id, database_name ):
-    #TODO: allow multiple FASTA input files
+def download_from_history(data_manager_dict, params, target_directory, database_id, database_name):
+    # TODO: allow multiple FASTA input files
     input_filename = params['param_dict']['reference_source']['input_fasta']
-    if isinstance( input_filename, list ):
-        fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
+    if isinstance(input_filename, list):
+        fasta_reader = [open(filename, 'rb') for filename in input_filename]
     else:
-        fasta_reader = open( input_filename )
-    
-    data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, database_id, database_name, params )
-    _add_data_table_entry( data_manager_dict, data_table_entry )
+        fasta_reader = open(input_filename)
+
+    data_table_entry = _stream_fasta_to_file(fasta_reader, target_directory, database_id, database_name, params)
+    _add_data_table_entry(data_manager_dict, data_table_entry)
 
 
-def copy_from_directory( data_manager_dict, params, target_directory, database_id, database_name ):
+def copy_from_directory(data_manager_dict, params, target_directory, database_id, database_name):
     input_filename = params['param_dict']['reference_source']['fasta_filename']
     create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink'
     if create_symlink:
-        data_table_entry = _create_symlink( input_filename, target_directory, database_id, database_name )
+        data_table_entry = _create_symlink(input_filename, target_directory, database_id, database_name)
     else:
-        if isinstance( input_filename, list ):
-            fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
+        if isinstance(input_filename, list):
+            fasta_reader = [open(filename, 'rb') for filename in input_filename]
         else:
-            fasta_reader = open( input_filename )    
-        data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, database_id, database_name, params )
-    _add_data_table_entry( data_manager_dict, data_table_entry )
+            fasta_reader = open(input_filename)
+        data_table_entry = _stream_fasta_to_file(fasta_reader, target_directory, database_id, database_name, params)
+    _add_data_table_entry(data_manager_dict, data_table_entry)
 
 
-def _add_data_table_entry( data_manager_dict, data_table_entry ):
-    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
-    data_manager_dict['data_tables']['diamond_database'] = data_manager_dict['data_tables'].get( 'diamond_database', [] )
-    data_manager_dict['data_tables']['diamond_database'].append( data_table_entry )
+def _add_data_table_entry(data_manager_dict, data_table_entry):
+    data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
+    data_manager_dict['data_tables']['diamond_database'] = data_manager_dict['data_tables'].get('diamond_database', [])
+    data_manager_dict['data_tables']['diamond_database'].append(data_table_entry)
     return data_manager_dict
 
 
-def _stream_fasta_to_file( fasta_stream, target_directory, database_id, database_name, params, close_stream=True ):
+def _stream_fasta_to_file(fasta_stream, target_directory, database_id, database_name, params, close_stream=True):
     fasta_base_filename = "%s.fa" % database_id
-    fasta_filename = os.path.join( target_directory, fasta_base_filename )
+    fasta_filename = os.path.join(target_directory, fasta_base_filename)
 
-    temp_fasta = tempfile.NamedTemporaryFile( delete=False, suffix=".fasta" )
+    temp_fasta = tempfile.NamedTemporaryFile(delete=False, suffix=".fasta")
     temp_fasta.close()
-    fasta_writer = open( temp_fasta.name, 'wb+' )
+    fasta_writer = open(temp_fasta.name, 'wb+')
 
-    if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1:
+    if isinstance(fasta_stream, list) and len(fasta_stream) == 1:
         fasta_stream = fasta_stream[0]
 
-    if isinstance( fasta_stream, list ):
+    if isinstance(fasta_stream, list):
         last_char = None
         for fh in fasta_stream:
-            if last_char not in [ None, '\n', '\r' ]:
-                fasta_writer.write( '\n' )
+            if last_char not in [None, '\n', '\r']:
+                fasta_writer.write('\n')
             while True:
-                data = fh.read( CHUNK_SIZE )
+                data = fh.read(CHUNK_SIZE)
                 if data:
-                    fasta_writer.write( data )
+                    fasta_writer.write(data)
                     last_char = data[-1]
                 else:
                     break
@@ -173,9 +173,9 @@
                 fh.close()
     else:
         while True:
-            data = fasta_stream.read( CHUNK_SIZE )
+            data = fasta_stream.read(CHUNK_SIZE)
             if data:
-                fasta_writer.write( data )
+                fasta_writer.write(data)
             else:
                 break
         if close_stream:
@@ -183,56 +183,58 @@
 
     fasta_writer.close()
 
-    args = [ 'diamond', 'makedb', '--in', temp_fasta.name, '--db', fasta_filename]
+    args = ['diamond', 'makedb', '--in', temp_fasta.name, '--db', fasta_filename]
 
-    tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-diamond-database-builder-stderr" )
-    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
+    tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-diamond-database-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 diamond database:"
         while True:
-            chunk = tmp_stderr.read( CHUNK_SIZE )
+            chunk = tmp_stderr.read(CHUNK_SIZE)
             if not chunk:
                 break
-            sys.stderr.write( chunk )
-        sys.exit( return_code )
+            sys.stderr.write(chunk)
+        sys.exit(return_code)
     tmp_stderr.close()
-    os.remove( temp_fasta.name )
-    return dict( value=database_id, name=database_name, db_path="%s.dmnd" % fasta_base_filename )
+    os.remove(temp_fasta.name)
+    return dict(value=database_id, name=database_name, db_path="%s.dmnd" % fasta_base_filename)
 
 
-def _create_symlink( input_filename, target_directory, database_id, database_name ):
+def _create_symlink(input_filename, target_directory, database_id, database_name):
     fasta_base_filename = "%s.fa" % database_id
-    fasta_filename = os.path.join( target_directory, fasta_base_filename )
-    os.symlink( input_filename, fasta_filename )
-    return dict( value=database_id, name=database_name, db_path=fasta_base_filename )
+    fasta_filename = os.path.join(target_directory, fasta_base_filename)
+    os.symlink(input_filename, fasta_filename)
+    return dict(value=database_id, name=database_name, db_path=fasta_base_filename)
 
 
-REFERENCE_SOURCE_TO_DOWNLOAD = dict( ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory )
+REFERENCE_SOURCE_TO_DOWNLOAD = dict(ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory)
+
 
 def main():
-    #Parse Command Line
+    # Parse Command Line
     parser = optparse.OptionParser()
-    parser.add_option( '-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description' )
+    parser.add_option('-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description')
     (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 )
+
+    params = json.loads(open(filename).read())
+    target_directory = params['output_data'][0]['extra_files_path']
+    os.mkdir(target_directory)
     data_manager_dict = {}
 
     database_id = params['param_dict']['database_id']
     database_name = params['param_dict']['database_name']
 
-    #Fetch the FASTA
-    REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, database_id, database_name )
-    
-    #save info to json file
-    open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
+    # Fetch the FASTA
+    REFERENCE_SOURCE_TO_DOWNLOAD[params['param_dict']['reference_source']['reference_source_selector']](data_manager_dict, params, target_directory, database_id, database_name)
+
+    # save info to json file
+    open(filename, 'w').write(json.dumps(data_manager_dict, sort_keys=True))
+
 
 if __name__ == "__main__":
     main()
--- 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
@@ -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>
--- /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
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/diamond_database.loc	Tue Dec 03 17:39:48 2019 -0500
@@ -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.
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX174.fasta	Tue Dec 03 17:39:48 2019 -0500
@@ -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
+
--- /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
@@ -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>
--- a/tool_dependencies.xml	Sun Feb 08 10:05:20 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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>