Mercurial > repos > dpryan79 > data_manager_bwameth_index_builder
changeset 1:f5a15a12a4c9 draft default tip
Uploaded
| author | dpryan79 |
|---|---|
| date | Thu, 15 Sep 2016 05:58:04 -0400 |
| parents | a801458261bb |
| children | |
| files | data_manager/bwameth_index_builder.py data_manager/bwameth_index_builder.xml tool_dependencies.xml |
| diffstat | 3 files changed, 11 insertions(+), 3 deletions(-) [+] |
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--- a/data_manager/bwameth_index_builder.py Thu Sep 15 04:59:28 2016 -0400 +++ b/data_manager/bwameth_index_builder.py Thu Sep 15 05:58:04 2016 -0400 @@ -11,14 +11,14 @@ DEFAULT_DATA_TABLE_NAME = "bwameth_indexes" -def build_hisat_index(data_manager_dict, params, args): +def build_bwameth_index(data_manager_dict, params, args): data_table_name = args.data_table_name target_directory = params[ 'output_data' ][0]['extra_files_path'] if not os.path.exists( target_directory ): os.mkdir( target_directory ) fasta_base_name = os.path.basename(args.fasta_filename) sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name) - os.symlink(options.fasta_filename, sym_linked_fasta_filename) + os.symlink(args.fasta_filename, sym_linked_fasta_filename) args = ['bwameth.py', 'index', sym_linked_fasta_filename] proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) return_code = proc.wait() @@ -55,7 +55,7 @@ raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (args.dbkey)) # build the index - build_hisat_index(data_manager_dict, args) + build_bwameth_index(data_manager_dict, params, args) # save info to json file open(filename, 'wb').write(dumps(data_manager_dict))
--- a/data_manager/bwameth_index_builder.xml Thu Sep 15 04:59:28 2016 -0400 +++ b/data_manager/bwameth_index_builder.xml Thu Sep 15 05:58:04 2016 -0400 @@ -1,6 +1,8 @@ <tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0"> <description>builder</description> <requirements> + <requirement type="package" version="0.7.12">bwa</requirement> + <requirement type="package" version="1.2">samtools</requirement> <requirement type="package" version="0.2.0">bwameth</requirement> </requirements> <command detect_errors="aggressive"><![CDATA[
--- a/tool_dependencies.xml Thu Sep 15 04:59:28 2016 -0400 +++ b/tool_dependencies.xml Thu Sep 15 05:58:04 2016 -0400 @@ -1,5 +1,11 @@ <?xml version="1.0"?> <tool_dependency> + <package name="bwa" version="0.7.12"> + <repository changeset_revision="67aa12c8d449" name="package_bwa_0_7_12" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="samtools" version="1.2"> + <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> <package name="bwameth" version="0.2.0"> <repository changeset_revision="fd470f9ef129" name="package_python_2_7_bwameth_0_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package>