# HG changeset patch
# User iuc
# Date 1733381341 0
# Node ID 9c91b5015dd32c384b4decc7b67d1fbba066c709
# Parent 39a922d01b0d962452d568f42181d6a0e9484383
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
diff -r 39a922d01b0d -r 9c91b5015dd3 data_manager/bowtie_color_space_index_builder.xml
--- a/data_manager/bowtie_color_space_index_builder.xml Tue May 21 07:35:37 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-
- builder
-
- bowtie
- python
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- 10.1186/gb-2009-10-3-r25
-
-
diff -r 39a922d01b0d -r 9c91b5015dd3 data_manager/bowtie_index_builder.py
--- a/data_manager/bowtie_index_builder.py Tue May 21 07:35:37 2024 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,99 +0,0 @@
-#!/usr/bin/env python
-from __future__ import print_function
-
-import json
-import optparse
-import os
-import subprocess
-import sys
-import tempfile
-
-CHUNK_SIZE = 2**20
-
-DEFAULT_DATA_TABLE_NAME = "bowtie_indexes"
-
-
-def get_id_name(params, dbkey, fasta_description=None):
- # 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
-
- sequence_name = params['param_dict']['sequence_name']
- if not sequence_name:
- sequence_name = fasta_description
- if not sequence_name:
- sequence_name = dbkey
- return sequence_id, sequence_name
-
-
-def build_bowtie_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME, color_space=False):
- # TODO: allow multiple FASTA input files
- fasta_base_name = os.path.split(fasta_filename)[-1]
- sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
- os.symlink(fasta_filename, sym_linked_fasta_filename)
- args = ['bowtie-build']
- if color_space:
- args.append('-C')
- args.append(sym_linked_fasta_filename)
- args.append(fasta_base_name)
- args.append(sym_linked_fasta_filename)
- tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-bowtie-index-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("Error building index:", file=sys.stderr)
- while True:
- chunk = tmp_stderr.read(CHUNK_SIZE)
- if not chunk:
- break
- sys.stderr.write(chunk)
- sys.exit(return_code)
- tmp_stderr.close()
- data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name)
- _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
-
-
-def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
- 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(data_table_name, [])
- data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
- return data_manager_dict
-
-
-def main():
- parser = optparse.OptionParser()
- parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename')
- parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey')
- parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description')
- parser.add_option('-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name')
- parser.add_option('-c', '--color_space', dest='color_space', action='store_true', default=False, help='color_space')
- (options, args) = parser.parse_args()
-
- filename = args[0]
-
- with open(filename) as fh:
- params = json.load(fh)
- target_directory = params['output_data'][0]['extra_files_path']
- os.mkdir(target_directory)
- data_manager_dict = {}
-
- dbkey = options.fasta_dbkey
-
- if dbkey in [None, '', '?']:
- raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
-
- sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
-
- # build the index
- build_bowtie_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME, color_space=options.color_space)
-
- # save info to json file
- with open(filename, 'w') as fh:
- json.dump(data_manager_dict, fh, sort_keys=True)
-
-
-if __name__ == "__main__":
- main()
diff -r 39a922d01b0d -r 9c91b5015dd3 data_manager/bowtie_index_builder.xml
--- a/data_manager/bowtie_index_builder.xml Tue May 21 07:35:37 2024 +0000
+++ b/data_manager/bowtie_index_builder.xml Thu Dec 05 06:49:01 2024 +0000
@@ -1,17 +1,39 @@
-
+
builder
+
+ 1.3.1
+ 0
+
- bowtie
- python
+ bowtie
+ #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
+ mkdir -p '${out_file.extra_files_path}' &&
+ ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' &&
+ bowtie-build '${out_file.extra_files_path}/${fasta_file_name}' '${out_file.extra_files_path}/${fasta_file_name}' &&
+ cp '$dmjson' '$out_file'
+ ]]>
+
+
+
+
@@ -22,6 +44,18 @@
+
+
+
+
+
+
+
+
+
+
+
+
- ${dbkey}/bowtie_index
+ genomes/${dbkey}/bowtie_index/v1/${value}
- ${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bowtie_index/${path}
- abspath
-
-
-
-
-
-
-
diff -r 39a922d01b0d -r 9c91b5015dd3 test-data/all_fasta.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc Thu Dec 05 06:49:01 2024 +0000
@@ -0,0 +1,19 @@
+#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):
+#
+#
+#
+#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.
+#
+phiX174 phiX174 phiX 174 ${__HERE__}/phiX174.fasta
diff -r 39a922d01b0d -r 9c91b5015dd3 test-data/bowtie_data_manager.1.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bowtie_data_manager.1.json Thu Dec 05 06:49:01 2024 +0000
@@ -0,0 +1,12 @@
+{
+ "data_tables":{
+ "bowtie_indexes":[
+ {
+ "value": "phiX174",
+ "dbkey": "phiX174",
+ "name": "phiX 174",
+ "path": "phiX174.fasta"
+ }
+ ]
+ }
+}
diff -r 39a922d01b0d -r 9c91b5015dd3 test-data/bowtie_data_manager.2.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bowtie_data_manager.2.json Thu Dec 05 06:49:01 2024 +0000
@@ -0,0 +1,12 @@
+{
+ "data_tables":{
+ "bowtie_indexes":[
+ {
+ "value": "tigHai1",
+ "dbkey": "phiX174",
+ "name": "Galeocerdo cuvier",
+ "path": "phiX174.fasta"
+ }
+ ]
+ }
+}
diff -r 39a922d01b0d -r 9c91b5015dd3 test-data/bowtie_indices.loc
diff -r 39a922d01b0d -r 9c91b5015dd3 test-data/phiX174.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX174.fasta Thu Dec 05 06:49:01 2024 +0000
@@ -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 39a922d01b0d -r 9c91b5015dd3 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Tue May 21 07:35:37 2024 +0000
+++ b/tool_data_table_conf.xml.sample Thu Dec 05 06:49:01 2024 +0000
@@ -9,9 +9,4 @@
value, dbkey, name, path
-
-
- value, dbkey, name, path
-
-
diff -r 39a922d01b0d -r 9c91b5015dd3 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Thu Dec 05 06:49:01 2024 +0000
@@ -0,0 +1,12 @@
+
+
+
+ value, dbkey, name, path
+
+
+
+
+ value, dbkey, name, path
+
+
+