Mercurial > repos > devteam > data_manager_fetch_index_maf
changeset 0:475b10cd2ae8 draft default tip
Uploaded
| author | devteam |
|---|---|
| date | Tue, 09 Jun 2020 14:27:06 -0400 |
| parents | |
| children | |
| files | .shed.yml README data_manager/data_manager_fetch_and_index_maf.py data_manager/data_manager_fetch_and_index_maf.xml data_manager_conf.xml test-data/phiX174.data_manager_json test-data/phiX174.fasta test-data/test.tar.bz2 tool-data/maf_index.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 10 files changed, 396 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Tue Jun 09 14:27:06 2020 -0400 @@ -0,0 +1,10 @@ +categories: +- Data Managers +description: Allows optionally defining a new DBKEY and retrieves a FASTA file and + populate the all_fasta.loc data table. +homepage_url: '' +long_description: '' +name: data_manager_fetch_genome_dbkeys_all_fasta +owner: devteam +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta +type: unrestricted
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue Jun 09 14:27:06 2020 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_fetch_and_index_maf.py Tue Jun 09 14:27:06 2020 -0400 @@ -0,0 +1,224 @@ +#!/usr/bin/env python +import bz2 +import ftplib +import gzip +import json +import optparse +import os +import re +import shutil +import subprocess +import sys +import tempfile +import urllib.parse +import urllib.request +import zipfile +from binascii import hexlify + +CHUNK_SIZE = 2**20 + +DEFAULT_DATA_TABLE_NAME = "indexed_maf_files" + +# Nice solution to opening compressed files (zip/bz2/gz) transparently +# https://stackoverflow.com/a/13045892/638445 + +class CompressedFile(object): + magic = None + file_type = None + mime_type = None + proper_extension = None + + def __init__(self, f): + # f is an open file or file like object + self.f = f + self.accessor = self.open() + + @classmethod + def is_magic(self, data): + print('%s: %s (m) <=> %s (f)' % (self.file_type, hexlify(self.magic).decode(), hexlify(data[:4]).decode())) + return hexlify(data).startswith(hexlify(self.magic)) + + def open(self): + return None + + +class ZIPFile(CompressedFile): + magic = b'\x50\x4b\x03\x04' + file_type = 'zip' + mime_type = 'compressed/zip' + + def open(self): + return zipfile.ZipFile(self.f) + + +class BZ2File(CompressedFile): + magic = b'\x42\x5a\x68' + file_type = 'bz2' + mime_type = 'compressed/bz2' + + def open(self): + return bz2.BZ2File(self.f) + + +class GZFile(CompressedFile): + magic = b'\x1f\x8b\x08' + file_type = 'gz' + mime_type = 'compressed/gz' + + def open(self): + return gzip.GzipFile(self.f) + + +# factory function to create a suitable instance for accessing files +def get_compressed_file(filename): + with open(filename, 'rb') as f: + print('seek: %d' % f.tell()) + start_of_file = f.read(16) + f.seek(0) + for cls in (ZIPFile, BZ2File, GZFile): + if cls.is_magic(start_of_file): + f.close() + return cls(filename) + + return None + +def url_download(url, tmp=False, localpath=None): + """Attempt to download gene annotation file from a given url + :param url: full url to gene annotation file + :type url: str. + :returns: name of downloaded gene annotation file + :raises: ContentDecodingError, IOError + """ + + # Generate file_name + file_name = url.split('/')[-1] + if tmp: + file_name = os.path.join(tempfile.mkdtemp(), file_name) + elif localpath is not None: + file_name = os.path.join(localpath, file_name) + + try: + # download URL (FTP and HTTP work, probably local and data too) + urllib.request.urlretrieve(url, file_name) + + # uncompress file if needed + cf = get_compressed_file(file_name) + print('cf: %s' % str(cf)) + if cf is not None: + uncompressed_file_name = os.path.splitext(file_name)[0] + with open(uncompressed_file_name, 'wb') as uncompressed_file: + shutil.copyfileobj(cf.accessor, uncompressed_file) + os.remove(file_name) + file_name = uncompressed_file_name + print(file_name) + except IOError as e: + sys.stderr.write('Error occured downloading reference file: %s' % e) + os.remove(file_name) + return file_name + + +def generate_metadata(params, options): + #3-way multiZ (hg18,panTro2,rheMac2) 3_WAY_MULTIZ_hg18 hg18,panTro2,rheMac2 hg18,panTro2,rheMac2 /PATH/chrM.maf,/PATH/chrX.maf,/PATH/chrY.maf + name = options.name + uid = name + species = [] + # Found to be the fastest way to strip non-alphanumeric characters + # from a string by some person on StackOverflow + pattern = re.compile('[\W]+') + uid = pattern.sub('_', uid).strip('_') + url = options.nexus + with open(url_download(url, True), 'r') as fh: + species = [line.strip(' (),').split(':')[0] for line in fh.readlines()] + return name, uid.upper(), species + +def get_maf_listing(maf_path): + maf_files = [] + maf_url = urllib.parse.urlparse(maf_path) + f = ftplib.FTP() + f.connect(maf_url.netloc) + f.login() + listing = f.mlsd(maf_url.path) + # print('\n'.join(['%s\t%s' % (name, facts['size']) for name, facts in listing])) + # exit(0) + for name, facts in listing: + # Remove this before PR + if int(facts['size']) > 74007: + continue + if not name.endswith('gz'): + continue + if facts['type'] != 'file': + continue + skip = False + for compression in ['gz', 'bz2', 'zip']: + for exclusion in ['_alt', '_random']: + if name.endswith('%s.maf.%s' % (exclusion, compression)): + skip = True + break + if skip: + continue + # if name.startswith('chrUn'): + # continue + maf_files.append(urllib.parse.urljoin(maf_path, name)) + f.close() + return maf_files + + +def index_maf_files(maf_files, maf_path, options, params, target_directory): + maf_paths = [] + for maf_file in maf_files: + maf_url = urllib.parse.urljoin(maf_path, maf_file) + local_maf = url_download(maf_url, target_directory) + print(os.path.realpath(local_maf)) + # exit(0) + index_command = ['maf_build_index.py', local_maf, local_maf + '.index'] + executor = subprocess.Popen(index_command) + stdout, stderr = executor.communicate() + print(stderr, file=sys.stderr) + + +def main(): + parser = optparse.OptionParser() + parser.add_option('-x', '--nexus', dest='nexus', action='store', type='string', help='URL for .nh') + parser.add_option('-a', '--alignments', dest='alignments', action='store', type='string', help='URL for alignments') + parser.add_option('-n', '--name', dest='name', action='store', type='string', help='Name') + parser.add_option('-o', '--output', dest='output', action='store', type='string', help='Output') + (options, args) = parser.parse_args() + + params = {} + + # with open(options.output) as fh: + # params = json.load(fh) + # target_directory = params['output_data'][0]['extra_files_path'] + target_directory = os.getcwd() + # if not os.path.exists(target_directory): + # os.mkdir(target_directory) + + display_name, uid, species_list = generate_metadata(params, options) + print('%s %s %s' % (display_name, uid, ','.join(species_list))) + maf_path = urllib.parse.urljoin(options.nexus, 'maf/') + maf_files = get_maf_listing(maf_path) + + data_manager_entry = { + 'data_tables': { + 'indexed_maf_files': { + 'display_name': display_name, + 'value': uid, + 'indexed_for': ','.join(species_list), + 'exists_in_maf': ','.join(species_list), + 'path': ','.join([os.path.join(target_directory, maf_file.split('/')[-1]) for maf_file in maf_files]) + } + } + } + + # Fetch the MAFs + index_maf_files(maf_files, maf_path, options, params, target_directory) + + print(json.dumps(data_manager_entry)) + + # with open(options.output, 'wb') as fh: + # fh.write(json.dumps(data_manager_entry)) + # open(filename, 'wb').write(json.dumps(data_manager_entry)) + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_fetch_and_index_maf.xml Tue Jun 09 14:27:06 2020 -0400 @@ -0,0 +1,35 @@ +<tool id="data_manager_fetch_and_index_maf" name="Fetch and index" version="1.0.0" tool_type="manage_data" profile="19.01"> + <description>multiple alignments from NCBI</description> + <requirements> + <requirement type="package" version="3.7">python</requirement> + <requirement type="package" version="0.8.8">bx-python</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/data_manager_fetch_and_index_maf.py' --nexus '$nexus' + --alignments '$alignments' --name '$name' --output '$output' + ]]></command> + <inputs> + <param name="dbkey" type="select" label="Species aligned against"> + <options from_data_table="all_fasta"/> + </param> + <param name="nexus" type="text" label="FTP path to nexus file on UCSC." help="The MAF paths will be computed from this" /> + <param name="name" type="text" label="Display name for this multi-alignment" /> + </inputs> + <outputs> + <data name="output" format="data_manager_json"/> + </outputs> + <tests> + <test /> + </tests> + <help> +**What it does** + +Fetches a multiple alignment from UCSC's FTP server and indexes it with bx-python. + +------ + +.. class:: infomark + +**Notice:** If you leave name, description, or id blank, it will be generated automatically. + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Tue Jun 09 14:27:06 2020 -0400 @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<data_managers> + + <data_manager tool_file="data_manager/data_manager_fetch_and_index_maf.xml" id="data_manager_fetch_and_index_maf"> + <data_table name="indexed_maf_files"> + <output> + <column name="name" /> + <column name="value" /> + <column name="indexed_for" /> + <column name="exists_in_maf" /> + <column name="path" output_ref="out_file" > + <move type="directory" relativize_symlinks="True"> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/align/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/align/${value}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX174.data_manager_json Tue Jun 09 14:27:06 2020 -0400 @@ -0,0 +1,1 @@ +{"data_tables": {"__dbkeys__": [{"len_path": "phiX174.len", "name": "phiX174", "value": "phiX174"}], "all_fasta": [{"dbkey": "phiX174", "name": "phiX174 sequence name", "path": "phix174.fa", "value": "phix174"}]}} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX174.fasta Tue Jun 09 14:27:06 2020 -0400 @@ -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/maf_index.loc.sample Tue Jun 09 14:27:06 2020 -0400 @@ -0,0 +1,17 @@ +#This is a sample file distributed with Galaxy that is used by some +#alignment tools. The maf_index.loc file has this format (white space +#characters are TAB characters): +# +#<Display_name UID> <indexed_for:build1,build2,build3> <exists_in_maf:build1,build2,build3> <Comma_Separated_List_of_Full_Paths_To_Files> +# +#ENCODE TBA (hg17) ENCODE_TBA_hg17 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 /depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm001/human.ENm001.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm002/human.ENm002.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm003/human.ENm003.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm004/human.ENm004.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm005/human.ENm005.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm006/human.ENm006.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm007/human.ENm007.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm008/human.ENm008.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm009/human.ENm009.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm010/human.ENm010.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm011/human.ENm011.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm012/human.ENm012.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm013/human.ENm013.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENm014/human.ENm014.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr111/human.ENr111.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr112/human.ENr112.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr113/human.ENr113.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr114/human.ENr114.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr121/human.ENr121.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr122/human.ENr122.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr123/human.ENr123.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr131/human.ENr131.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr132/human.ENr132.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr133/human.ENr133.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr211/human.ENr211.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr212/human.ENr212.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr213/human.ENr213.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr221/human.ENr221.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr222/human.ENr222.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr223/human.ENr223.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr231/human.ENr231.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr232/human.ENr232.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr233/human.ENr233.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr311/human.ENr311.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr312/human.ENr312.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr313/human.ENr313.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr321/human.ENr321.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr322/human.ENr322.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr323/human.ENr323.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr324/human.ENr324.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr331/human.ENr331.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr332/human.ENr332.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr333/human.ENr333.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/tba/ENr334/human.ENr334.maf +#ENCODE MAVID (hg17) ENCODE_MAVID_hg17 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant,fr1,galago,hedgehog,hg17,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 /depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm001.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm002.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm003.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm004.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm005.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm006.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm007.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm008.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm009.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm010.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm011.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm012.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm013.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENm014.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr111.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr112.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr113.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr114.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr121.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr122.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr123.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr131.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr132.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr133.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr211.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr212.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr213.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr221.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr222.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr223.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr231.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr232.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr233.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr311.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr312.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr313.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr321.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr322.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr323.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr324.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr331.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr332.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr333.maf,/depot/data2/galaxy/hg17/align/encode_relabeled/mavid/abs/ENr334.maf +#ENCODE TBA (hg16) ENCODE_TBA_hg16 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant=elephant,fr1,galago,hedgehog,hg16,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 armadillo,baboon,galGal2,panTro1,colobus_monkey,cow,canFam1,dusky_titi,elephant=elephant,fr1,galago,hedgehog,hg16,rheMac1,marmoset,monDom1,mm6,mouse_lemur,owl_monkey,platypus,rabbit,rn3,rfbat,shrew,tenrec,tetNig1,xenTro1,danRer2 /depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm001.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm002.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm003.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm004.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm005.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm006.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm007.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm008.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm009.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm010.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm011.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm012.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm013.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENm014.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr111.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr112.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr113.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr114.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr121.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr122.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr123.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr131.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr132.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr133.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr211.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr212.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr213.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr221.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr222.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr223.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr231.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr232.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr233.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr311.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr312.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr313.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr321.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr322.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr323.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr324.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr331.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr332.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr333.maf,/depot/data2/galaxy/hg16/align/encode/june2005freeze/tba/human.ENr334.maf +#8-way multiZ (hg17) 8_WAY_MULTIZ_hg17 canFam1,danRer1,fr1,galGal2,hg17,mm5,panTro1,rn3 canFam1,danRer1,fr1,galGal2,hg17,mm5,panTro1,rn3 /depot/data2/galaxy/hg17/align/8way-multiZ/chr1.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr1_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr10.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr10_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr11.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr12.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr12_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr13.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr13_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr14.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr15.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr15_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr16.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr16_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr17.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr17_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr18.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr18_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr19.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr19_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr2.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr2_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr20.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr21.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr22.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr22_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr3.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr3_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr4.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr4_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr5.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr5_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr6.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr6_hla_hap1.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr6_hla_hap2.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr6_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr7.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr7_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr8.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr8_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr9.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chr9_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chrM.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chrX.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chrX_random.maf,/depot/data2/galaxy/hg17/align/8way-multiZ/chrY.maf +#17-way multiZ (hg18) 17_WAY_MULTIZ_hg18 hg18,panTro1,bosTau2,rheMac2,mm8,rn4,canFam2,echTel1,loxAfr1,oryCun1,danRer3,monDom4,dasNov1,galGal2,fr1,tetNig1,xenTro1 hg18,panTro1,bosTau2,rheMac2,mm8,rn4,canFam2,echTel1,loxAfr1,oryCun1,danRer3,monDom4,dasNov1,galGal2,fr1,tetNig1,xenTro1 /depot/data2/galaxy/hg18/align/17way-multiZ/chr10.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr10_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr11.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr11_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr12.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr13.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr13_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr14.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr15.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr15_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr16.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr16_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr17.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr17_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr18.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr18_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr19.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr19_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr1.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr1_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr20.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr21.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr21_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr22_h2_hap1.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr22.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr22_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr2.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr2_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr3.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr3_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr4.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr4_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr5_h2_hap1.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr5.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr5_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr6_cox_hap1.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr6.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr6_qbl_hap2.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr6_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr7.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr7_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr8.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr8_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr9.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chr9_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chrM.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chrX.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chrX_random.maf,/depot/data2/galaxy/hg18/align/17way-multiZ/chrY.maf +#3-way multiZ (hg18,panTro2,rheMac2) 3_WAY_MULTIZ_hg18 hg18,panTro2,rheMac2 hg18,panTro2,rheMac2 /depot/data2/galaxy/hg18/align/3way-multiZ/chr10.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr10_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr11.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr11_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr12.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr13.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr13_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr14.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr15.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr15_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr16.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr16_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr17.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr17_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr18.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr18_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr19.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr19_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr1.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr1_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr20.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr21.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr21_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr22_h2_hap1.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr22.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr22_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr2.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr2_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr3.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr3_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr4.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr4_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr5_h2_hap1.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr5.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr5_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr6_cox_hap1.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr6.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr6_qbl_hap2.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr6_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr7.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr7_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr8.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr8_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr9.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chr9_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chrM.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chrX.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chrX_random.maf,/depot/data2/galaxy/hg18/align/3way-multiZ/chrY.maf +#5-way multiZ (hg18,panTro2,rheMac2,mm8,canFam2) 5_WAY_MULTIZ_hg18 hg18,panTro2,rheMac2,mm8,canFam2 hg18,panTro2,rheMac2,mm8,canFam2 /depot/data2/galaxy/hg18/align/5way-multiZ/chr10.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr10_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr11.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr11_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr12.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr13.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr13_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr14.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr15.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr15_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr16.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr16_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr17.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr17_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr18.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr18_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr19.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr19_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr1.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr1_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr20.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr21.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr21_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr22_h2_hap1.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr22.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr22_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr2.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr2_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr3.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr3_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr4.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr4_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr5_h2_hap1.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr5.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr5_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr6_cox_hap1.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr6.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr6_qbl_hap2.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr6_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr7.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr7_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr8.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr8_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr9.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chr9_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chrM.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chrX.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chrX_random.maf,/depot/data2/galaxy/hg18/align/5way-multiZ/chrY.maf +#28-way multiZ (hg18) 28_WAY_MULTIZ_hg18 hg18 hg18,dasNov1,otoGar1,felCat3,galGal3,panTro2,bosTau3,canFam2,loxAfr1,xenTro2,fr2,cavPor2,eriEur1,equCab1,anoCar1,oryLat1,mm8,monDom4,ornAna1,oryCun1,rn4,rheMac2,sorAra1,gasAcu1,echTel1,tetNig1,tupBel1,danRer4 /depot/data2/galaxy/hg18/align/multiz28way/chr1.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr10.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr10_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr11.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr11_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr12.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr13.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr13_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr14.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr15.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr15_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr16.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr16_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr17.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr17_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr18.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr18_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr19.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr19_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr1_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr2.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr20.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr21.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr21_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr22.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr22_h2_hap1.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr22_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr2_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr3.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr3_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr4.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr4_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr5.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr5_h2_hap1.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr5_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr6.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr6_cox_hap1.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr6_qbl_hap2.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr6_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr7.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr7_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr8.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr8_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr9.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chr9_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chrM.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chrX.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chrX_random.maf.lzo,/depot/data2/galaxy/hg18/align/multiz28way/chrY.maf.lzo +#15-way multiZ (dm2) 15_WAY_MULTIZ_dm2 dm2,droSim1,droSec1,droYak2,droEre2,droAna3,dp4,droPer1,droWil1,droVir3,droMoj3,droGri2,anoGam1,apiMel2,triCas2 dm2,droSim1,droSec1,droYak2,droEre2,droAna3,dp4,droPer1,droWil1,droVir3,droMoj3,droGri2,anoGam1,apiMel2,triCas2 /depot/data2/galaxy/dm2/align/multiz15way/chr2L.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr2R.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr2h.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr3L.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr3R.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr3h.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr4.maf,/depot/data2/galaxy/dm2/align/multiz15way/chr4h.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrM.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrU.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrX.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrXh.maf,/depot/data2/galaxy/dm2/align/multiz15way/chrYh.maf +#17-way multiZ (mm8) 17_WAY_MULTIZ_mm8 mm8 hg18,panTro1,bosTau2,rheMac2,mm8,rn4,canFam2,echTel1,loxAfr1,oryCun1,danRer3,monDom4,dasNov1,galGal2,fr1,tetNig1,xenTro1 /depot/data2/galaxy/mm8/align/multiz17way/chr10.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr10_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr11.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr12.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr13.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr13_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr14.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr15.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr15_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr16.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr17.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr17_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr18.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr19.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr1.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr1_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr2.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr3.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr4.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr5.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr5_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr6.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr7.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr7_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr8.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr8_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr9.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chr9_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrM.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrUn_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrX.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrX_random.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrY.maf.lzo,/depot/data2/galaxy/mm8/align/multiz17way/chrY_random.maf.lzo +#8-way multiZ (ponAbe2) 8_WAY_MULTIZ_ponAbe2 ponAbe2,hg18,panTro2,rheMac2,calJac1,mm9,monDom4,ornAna1 ponAbe2,hg18,panTro2,rheMac2,calJac1,mm9,monDom4,ornAna1 /depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr10.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr10_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr11.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr11_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr12.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr12_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr13.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr13_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr14.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr14_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr15.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr15_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr16.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr16_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr17.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr17_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr18.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr18_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr19.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr19_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr1_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr20.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr20_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr21.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr21_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr22.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr22_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2a.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2a_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2b.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr2b_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr3.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr3_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr4.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr4_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5_h2_hap1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr5_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_cox_hap1.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_cox_hap1_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_qbl_hap2.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_qbl_hap2_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr6_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr7.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr7_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr8.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr8_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr9.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chr9_random.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrM.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrUn.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrX.maf.lzo,/depot/data2/galaxy/ponAbe2/align/multiz8way/maf/chrX_random.maf.lzo
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jun 09 14:27:06 2020 -0400 @@ -0,0 +1,8 @@ +<!-- Paths are relative to the value of `tool_data_path` in galaxy.ini --> +<tables> + <!-- Locations of MAF files that have been indexed with bx-python --> + <table name="indexed_maf_files"> + <columns>name, value, indexed_for, exists_in_maf, path</columns> + <file path="maf_index.loc" /> + </table> +</tables>