Mercurial > repos > devteam > data_manager_sam_fasta_index_builder
changeset 3:a1756ea43ba1 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 10:19:05 -0400 |
| parents | 4551ccb17ca1 |
| children | 30fc567efa38 |
| files | README data_manager/data_manager_sam_fasta_index_builder.py tool_dependencies.xml |
| diffstat | 3 files changed, 3 insertions(+), 1 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue Oct 13 10:19:05 2015 -0400 @@ -0,0 +1,1 @@ +TODO
--- a/data_manager/data_manager_sam_fasta_index_builder.py Fri Mar 28 13:57:54 2014 -0400 +++ b/data_manager/data_manager_sam_fasta_index_builder.py Tue Oct 13 10:19:05 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 Fri Mar 28 13:57:54 2014 -0400 +++ b/tool_dependencies.xml Tue Oct 13 10:19:05 2015 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="samtools" version="0.1.19"> - <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>