Mercurial > repos > devteam > data_manager_sam_fasta_index_builder
changeset 2:2a1ac1abc3f7 draft
planemo upload commit 5ad726dc73203a704666033cd3bf70b82575978f
| author | devteam |
|---|---|
| date | Wed, 26 Aug 2015 13:22:37 -0400 |
| parents | cf875cbe2df4 |
| children | 1f54e98616af |
| files | data_manager/data_manager_sam_fasta_index_builder.py tool_dependencies.xml |
| diffstat | 2 files changed, 2 insertions(+), 1 deletions(-) [+] |
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--- a/data_manager/data_manager_sam_fasta_index_builder.py Thu Mar 27 15:08:42 2014 -0400 +++ b/data_manager/data_manager_sam_fasta_index_builder.py Wed Aug 26 13:22:37 2015 -0400 @@ -27,6 +27,7 @@ def build_sam_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ): #TODO: allow multiple FASTA input files + assert os.path.exists( fasta_filename ), 'FASTA file "%s" is missing, cannot build samtools index.' % fasta_filename 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 )
--- a/tool_dependencies.xml Thu Mar 27 15:08:42 2014 -0400 +++ b/tool_dependencies.xml Wed Aug 26 13:22:37 2015 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="samtools" version="0.1.19"> - <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>