# HG changeset patch
# User devteam
# Date 1422975930 18000
# Node ID c89e003f518a341f1aa5aac6c5115a8c35723b2e

Uploaded

diff -r 000000000000 -r c89e003f518a README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Tue Feb 03 10:05:30 2015 -0500
@@ -0,0 +1,1 @@
+Creates a New dbkey entry with .len files in __dbkeys__ and populates all_fasta tool datatables.
\ No newline at end of file
diff -r 000000000000 -r c89e003f518a data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py	Tue Feb 03 10:05:30 2015 -0500
@@ -0,0 +1,415 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+import sys
+import os
+import tempfile
+import shutil
+import optparse
+import urllib2
+#import uuid
+from ftplib import FTP
+import tarfile
+import zipfile
+import gzip
+import bz2
+
+from json import loads, dumps
+
+
+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 stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit(1)
+    
+def get_dbkey_dbname_id_name( params, dbkey_description=None ):
+    dbkey = params['param_dict']['dbkey_source']['dbkey']
+    #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 #uuid.uuid4() generate and use an uuid instead?
+    
+    if params['param_dict']['dbkey_source']['dbkey_source_selector'] == 'new':
+        dbkey_name = params['param_dict']['dbkey_source']['dbkey_name']
+        if not dbkey_name:
+            dbkey_name = dbkey
+    else:
+        dbkey_name = None
+    
+    sequence_name = params['param_dict']['sequence_name']
+    if not sequence_name:
+        sequence_name = dbkey_description
+        if not sequence_name:
+            sequence_name = dbkey
+    return dbkey, dbkey_name, sequence_id, sequence_name
+
+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 ]
+
+def _get_stream_readers_for_tar( file_obj, tmp_dir ):
+    fasta_tar = tarfile.open( fileobj=file_obj, mode='r:*' )
+    return filter( lambda x: x is not None, [ 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' )
+    rval = []
+    for member in fasta_zip.namelist():
+        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_bz2( file_obj, tmp_dir ):
+    return [ bz2.BZ2File( file_obj.name, 'rb' ) ]
+
+def sort_fasta( fasta_filename, sort_method, params ):
+    if sort_method is None:
+        return
+    assert sort_method in SORTING_METHODS, ValueError( "%s is not a valid sorting option." % sort_method )
+    return SORTING_METHODS[ sort_method ]( fasta_filename, params )
+
+def _move_and_index_fasta_for_sorting( fasta_filename ):
+    unsorted_filename = tempfile.NamedTemporaryFile().name
+    shutil.move( fasta_filename, unsorted_filename )
+    fasta_offsets = {}
+    unsorted_fh = open( unsorted_filename )
+    while True:
+        offset = unsorted_fh.tell()
+        line = unsorted_fh.readline()
+        if not line:
+            break
+        if line.startswith( ">" ):
+            line = line.split( None, 1 )[0][1:]
+            fasta_offsets[ line ] = offset
+    unsorted_fh.close()
+    current_order = map( lambda x: x[1], sorted( map( lambda x: ( x[1], x[0] ), fasta_offsets.items() ) ) )
+    return ( unsorted_filename, fasta_offsets, current_order )
+
+def _write_sorted_fasta( sorted_names, fasta_offsets, sorted_fasta_filename, unsorted_fasta_filename ):
+    unsorted_fh = open( unsorted_fasta_filename )
+    sorted_fh = open( sorted_fasta_filename, 'wb+' )
+    
+    for name in sorted_names:
+        offset = fasta_offsets[ name ]
+        unsorted_fh.seek( offset )
+        sorted_fh.write( unsorted_fh.readline() )
+        while True:
+            line = unsorted_fh.readline()
+            if not line or line.startswith( ">" ):
+                break
+            sorted_fh.write( line )
+    unsorted_fh.close()
+    sorted_fh.close()
+
+def _sort_fasta_as_is( fasta_filename, params ):
+    return
+
+def _sort_fasta_lexicographical( fasta_filename, params ):
+    ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
+    sorted_names = sorted( fasta_offsets.keys() )
+    if sorted_names == current_order:
+        shutil.move( unsorted_filename, fasta_filename )
+    else:
+        _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename )    
+
+def _sort_fasta_gatk( fasta_filename, params ):
+    #This method was added by reviewer request.
+    ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
+    sorted_names = map( str, range( 1, 23 ) ) + [ 'X', 'Y' ]
+    #detect if we have chrN, or just N
+    has_chr = False
+    for chrom in sorted_names:
+        if "chr%s" % chrom in current_order:
+            has_chr = True
+            break
+    
+    if has_chr:
+        sorted_names = map( lambda x: "chr%s" % x, sorted_names)
+        sorted_names.insert( 0, "chrM" )
+    else:
+        sorted_names.insert( 0, "MT" )
+    sorted_names.extend( map( lambda x: "%s_random" % x, sorted_names ) )
+    
+    existing_sorted_names = []
+    for name in sorted_names:
+        if name in current_order:
+            existing_sorted_names.append( name )
+    for name in current_order:
+        #TODO: confirm that non-canonical names do not need to be sorted specially
+        if name not in existing_sorted_names:
+            existing_sorted_names.append( name )
+    
+    if existing_sorted_names == current_order:
+        shutil.move( unsorted_filename, fasta_filename )
+    else:
+        _write_sorted_fasta( existing_sorted_names, fasta_offsets, fasta_filename, unsorted_filename )
+
+def _sort_fasta_custom( fasta_filename, params ):
+    ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
+    sorted_names = []
+    for id_repeat in params['param_dict']['sorting']['sequence_identifiers']:
+        sorted_names.append( id_repeat[ 'identifier' ] )
+    handle_not_listed = params['param_dict']['sorting']['handle_not_listed']['handle_not_listed_selector']
+    if handle_not_listed.startswith( 'keep' ):
+        add_list = []
+        for name in current_order:
+            if name not in sorted_names:
+                add_list.append( name )
+        if add_list:
+            if handle_not_listed == 'keep_append':
+                sorted_names.extend( add_list )
+            else:
+                add_list.extend( sorted_names )
+                sorted_names = add_list
+    if sorted_names == current_order:
+        shutil.move( unsorted_filename, fasta_filename )
+    else:
+        _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename )
+
+def download_from_ucsc( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ):
+    UCSC_FTP_SERVER = 'hgdownload.cse.ucsc.edu'
+    UCSC_DOWNLOAD_PATH = '/goldenPath/%s/bigZips/'
+    COMPRESSED_EXTENSIONS = [ ( '.tar.gz', _get_stream_readers_for_tar ), ( '.tar.bz2', _get_stream_readers_for_tar ), ( '.zip', _get_stream_readers_for_zip ), ( '.fa.gz', _get_stream_readers_for_gzip ), ( '.fa.bz2', _get_stream_readers_for_bz2 ) ]
+    
+    email = params['param_dict']['__user_email__']
+    if not email:
+        email = 'anonymous@example.com'
+
+    ucsc_dbkey = params['param_dict']['reference_source']['requested_dbkey'] or dbkey
+    UCSC_CHROM_FA_FILENAMES = [ '%s.chromFa' % ucsc_dbkey, 'chromFa' ]
+    
+    ftp = FTP( UCSC_FTP_SERVER )
+    ftp.login( 'anonymous', email )
+    
+    ucsc_path = UCSC_DOWNLOAD_PATH % ucsc_dbkey
+    path_contents = _get_files_in_ftp_path( ftp, ucsc_path )
+    
+    ucsc_file_name = None
+    get_stream_reader = None
+    ext = None
+    ucsc_chrom_fa_filename = None
+    for ucsc_chrom_fa_filename in UCSC_CHROM_FA_FILENAMES:
+        for ext, get_stream_reader in COMPRESSED_EXTENSIONS:
+            if "%s%s" % ( ucsc_chrom_fa_filename, ext ) in path_contents:
+                ucsc_file_name = "%s%s%s" % ( ucsc_path, ucsc_chrom_fa_filename, ext )
+                break
+        if ucsc_file_name:
+            break
+    
+    if not ucsc_file_name:
+        raise Exception( 'Unable to determine filename for UCSC Genome for %s: %s' % ( ucsc_dbkey, path_contents ) )
+    
+    
+    tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-ucsc-' )
+    ucsc_fasta_filename = os.path.join( tmp_dir, "%s%s" % ( ucsc_chrom_fa_filename, ext ) )
+    
+    fasta_base_filename = "%s.fa" % sequence_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( ucsc_fasta_filename, 'wb+' )
+    
+    ftp.retrbinary( 'RETR %s' % ucsc_file_name, tmp_fasta.write )
+    
+    tmp_fasta.flush()
+    tmp_fasta.seek( 0 )
+    
+    fasta_readers = get_stream_reader( tmp_fasta, tmp_extract_dir )
+    
+    for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ):
+        if data_table_entry:
+            _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
+    
+    for fasta_reader in fasta_readers:
+        fasta_reader.close()
+    tmp_fasta.close()
+    cleanup_before_exit( tmp_dir )
+
+def download_from_ncbi( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ):
+    NCBI_DOWNLOAD_URL = 'http://togows.dbcls.jp/entry/ncbi-nucleotide/%s.fasta' #FIXME: taken from dave's genome manager...why some japan site?
+    
+    requested_identifier = params['param_dict']['reference_source']['requested_identifier']
+    url = NCBI_DOWNLOAD_URL % requested_identifier
+    fasta_readers = urllib2.urlopen( url )
+    
+    for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ):
+        if data_table_entry:
+            _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
+
+def download_from_url( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_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_readers = [ urllib2.urlopen( url ) for url in urls ]
+    
+    for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ):
+        if data_table_entry:
+            _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
+
+def download_from_history( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ):
+    #TODO: allow multiple FASTA input files
+    input_filename = params['param_dict']['reference_source']['input_fasta']
+    if isinstance( input_filename, list ):
+        fasta_readers = [ open( filename, 'rb' ) for filename in input_filename ]
+    else:
+        fasta_readers = open( input_filename )
+    
+    for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ):
+        if data_table_entry:
+            _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
+
+def copy_from_directory( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_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_entries = _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name )
+    else:
+        if isinstance( input_filename, list ):
+            fasta_readers = [ open( filename, 'rb' ) for filename in input_filename ]
+        else:
+            fasta_readers = open( input_filename )    
+        data_table_entries = _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params )
+    for data_table_name, data_table_entry in data_table_entries:
+        if data_table_entry:
+            _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
+
+def _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ):
+    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( 'all_fasta', [] )
+    data_manager_dict['data_tables'][data_table_name].append( data_table_entry )
+    return data_manager_dict
+
+def _stream_fasta_to_file( fasta_stream, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params, close_stream=True ):
+    fasta_base_filename = "%s.fa" % sequence_id
+    fasta_filename = os.path.join( target_directory, fasta_base_filename )
+    fasta_writer = open( fasta_filename, 'wb+' )
+    
+    if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1:
+        fasta_stream = fasta_stream[0]
+    
+    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' )
+            while True:
+                data = fh.read( CHUNK_SIZE )
+                if data:
+                    fasta_writer.write( data )
+                    last_char = data[-1]
+                else:
+                    break
+            if close_stream:
+                fh.close()
+    else:
+        while True:
+            data = fasta_stream.read( CHUNK_SIZE )
+            if data:
+                fasta_writer.write( data )
+            else:
+                break
+        if close_stream:
+            fasta_stream.close()
+    
+    fasta_writer.close()
+    
+    sort_fasta( fasta_filename, params['param_dict']['sorting']['sort_selector'], params )
+    
+    dbkey_dict = None
+    if dbkey_name:
+        #do len calc here
+        len_base_name = "%s.len" % ( dbkey )
+        compute_fasta_length( fasta_filename, os.path.join( target_directory, len_base_name ), keep_first_word=True )
+        dbkey_dict = dict( value=dbkey, name=dbkey_name, len_path=len_base_name )
+    
+    return [ ( '__dbkeys__', dbkey_dict ), ( 'all_fasta', dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
+
+def compute_fasta_length( fasta_file, out_file, keep_first_word=False ):
+
+    infile = fasta_file
+    out = open( out_file, 'w')
+
+    fasta_title = ''
+    seq_len = 0
+
+    first_entry = True
+
+    for line in open( infile ):
+        line = line.strip()
+        if not line or line.startswith( '#' ):
+            continue
+        if line[0] == '>':
+            if first_entry == False:
+                if keep_first_word:
+                    fasta_title = fasta_title.split()[0]
+                out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) )
+            else:
+                first_entry = False
+            fasta_title = line
+            seq_len = 0
+        else:
+            seq_len += len(line)
+
+    # last fasta-entry
+    if keep_first_word:
+        fasta_title = fasta_title.split()[0]
+    out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) )
+    out.close()
+
+def _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ):
+    fasta_base_filename = "%s.fa" % sequence_id
+    fasta_filename = os.path.join( target_directory, fasta_base_filename )
+    os.symlink( input_filename, fasta_filename )
+    
+    dbkey_dict = None
+    if dbkey_name:
+        #do len calc here
+        len_base_name = "%s.len" % ( dbkey )
+        compute_fasta_length( fasta_filename, os.path.join( target_directory, len_base_name ), keep_first_word=True )
+        dbkey_dict = dict( value=dbkey, name=dbkey_name, len_path=len_base_name )
+    
+    return [ ( '__dbkeys__', dbkey_dict ), ( 'all_fasta', dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
+
+
+
+
+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 )
+
+SORTING_METHODS = dict( as_is=_sort_fasta_as_is, lexicographical=_sort_fasta_lexicographical, gatk=_sort_fasta_gatk, custom=_sort_fasta_custom )
+
+def main():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    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 = loads( open( filename ).read() )
+    target_directory = params[ 'output_data' ][0]['extra_files_path']
+    os.mkdir( target_directory )
+    data_manager_dict = {}
+    
+    dbkey, dbkey_name, sequence_id, sequence_name = get_dbkey_dbname_id_name( params, dbkey_description=options.dbkey_description ) 
+    
+    if dbkey in [ None, '', '?' ]:
+        raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
+    
+    #Fetch the FASTA
+    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 )
+    
+    #save info to json file
+    open( filename, 'wb' ).write( dumps( data_manager_dict ) )
+        
+if __name__ == "__main__": main()
diff -r 000000000000 -r c89e003f518a data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml	Tue Feb 03 10:05:30 2015 -0500
@@ -0,0 +1,116 @@
+<tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.1" tool_type="manage_data">
+    <description>fetching</description>
+    <command interpreter="python">data_manager_fetch_genome_all_fasta_dbkeys.py "${out_file}" 
+    #if str( $dbkey_source.dbkey_source_selector ) == 'existing':
+    --dbkey_description ${ dbkey_source.dbkey.get_display_text() }
+    #else
+    --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }"
+    #end if
+    
+    </command>
+    <inputs>
+        <conditional name="dbkey_source">
+          <param name="dbkey_source_selector" type="select" label="Use existing dbkey or create a new one.">
+            <option value="existing" selected="True">Existing</option>
+            <option value="new">New</option>
+          </param>
+          <when value="existing">
+              <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
+          </when>
+          <when value="new">
+              <param type="text" name="dbkey" value="" label="dbkey" optional="False" />
+              <param type="text" name="dbkey_name" value="" label="Display name for dbkey" />
+          </when>
+        </conditional>
+        
+        <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="ucsc" selected="True">UCSC</option>
+            <option value="ncbi">NCBI</option>
+            <option value="url">URL</option>
+            <option value="history">History</option>
+            <option value="directory">Directory on Server</option>
+          </param>
+          <when value="ucsc">
+            <param type="text" name="requested_dbkey" value="" label="UCSC's DBKEY for source FASTA" optional="False" />
+          </when>
+          <when value="ncbi">
+            <param type="text" name="requested_identifier" value="" label="NCBI identifier" optional="False" />
+          </when>
+          <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>
+        <conditional name="sorting">
+          <param name="sort_selector" type="select" label="Choose the source for the reference genome">
+            <option value="as_is" selected="True">As is</option>
+            <option value="lexicographical">Lexicographical</option>
+            <option value="gatk">GATK</option>
+            <option value="custom">Custom</option>
+          </param>
+          <when value="as_is">
+          </when>
+          <when value="lexicographical">
+          </when>
+          <when value="gatk">
+          </when>
+          <when value="custom">
+            <repeat name="sequence_identifiers" title="Sequence Identifiers" min="1" default="1">
+                <param type="text" name="identifier" value="" label="Sequence Identifier" optional="False" />
+            </repeat>
+            <conditional name="handle_not_listed">
+                <param name="handle_not_listed_selector" type="select" label="How to handle non-specified Identifiers">
+                    <option value="discard" selected="True">Discard</option>
+                    <option value="keep_append">Keep and Append</option>
+                    <option value="keep_prepend">Keep and Prepend</option>
+                </param>
+                <when value="discard">
+                </when>
+                <when value="keep_append">
+                </when>
+                <when value="keep_prepend">
+                </when>
+            </conditional>
+          </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 reference genome from various sources (UCSC, NCBI, URL, Galaxy History, or a server directory) and populates the "all_fasta" data table.
+
+------
+
+
+
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically. 
+
+    </help>
+</tool>
diff -r 000000000000 -r c89e003f518a data_manager_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Tue Feb 03 10:05:30 2015 -0500
@@ -0,0 +1,36 @@
+<?xml version="1.0"?>
+<data_managers>
+    
+    <data_manager tool_file="data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml" id="fetch_genome_all_fasta_dbkeys">
+        <data_table name="all_fasta">
+            <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}/seq/${path}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/seq/${path}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+        <data_table name="__dbkeys__">
+            <output>
+                <column name="value" />
+                <column name="name" />
+                <column name="len_path" output_ref="out_file" >
+                    <move type="file">
+                        <source>${len_path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}/len/${len_path}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/len/${len_path}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
+    
+</data_managers>
diff -r 000000000000 -r c89e003f518a test-data/phiX174.data_manager_json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX174.data_manager_json	Tue Feb 03 10:05:30 2015 -0500
@@ -0,0 +1,1 @@
+{"data_tables": {"all_fasta": [{"path": "anoGam1.fa", "dbkey": "anoGam1", "name": "A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1)", "value": "anoGam1"}]}}
\ No newline at end of file
diff -r 000000000000 -r c89e003f518a test-data/phiX174.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX174.fasta	Tue Feb 03 10:05:30 2015 -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
+
diff -r 000000000000 -r c89e003f518a tool-data/all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Tue Feb 03 10:05:30 2015 -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.
+#
diff -r 000000000000 -r c89e003f518a tool-data/dbkeys.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/dbkeys.loc.sample	Tue Feb 03 10:05:30 2015 -0500
@@ -0,0 +1,1 @@
+#<dbkey>		<display_name>	<len_file_path>
\ No newline at end of file
diff -r 000000000000 -r c89e003f518a tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Feb 03 10:05:30 2015 -0500
@@ -0,0 +1,12 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+    <!-- Locations of dbkeys and len files under genome directory -->
+    <table name="__dbkeys__" comment_char="#">
+        <columns>value, name, len_path</columns>
+        <file path="tool-data/dbkeys.loc" />
+    </table>
+</tables>