changeset 4:07fc4bf0cff4 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/add_ctat_ref_lib.py	Tue Dec 12 15:18:15 2017 -0500
@@ -0,0 +1,94 @@
+#!/usr/bin/env python
+# ref: https://galaxyproject.org/admin/tools/data-managers/how-to/define/
+
+# Rewritten by H.E. Cicada Brokaw Dennis from source downloaded from the toolshed.
+# Eventually this should be modified to allow downloading of more than just the one library,
+# to let the user select what library/location to download, but that would require the
+# download tool to generate the list of libraries to download on the fly. Currently
+# we are only using the one library.
+# Users can create other ones locally and use this tool to add them if they don't want
+# to add them by hand.
+
+import argparse
+import os
+import tarfile
+import urllib
+
+from galaxy.util.json import from_json_string, to_json_string
+
+# The following was used by prior program to get input parameters from the json.
+# Just leaving here for reference.
+#def get_reference_id_name(params):
+#    genome_id = params['param_dict']['genome_id']
+#    genome_name = params['param_dict']['genome_name']
+#    return genome_id, genome_name
+#
+#def get_url(params):
+#    trained_url = params['param_dict']['trained_url']
+#    return trained_url
+
+def download_from_BroadInst(destination):
+    ctat_resource_lib = 'https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v26_CTAT_lib_Nov012017.plug-n-play.tar.gz'
+    # FIX - Check that the download directory is empty if it exists. Also, can we check if there is enough space on the device as well?
+    # FIX - Also we want to make sure that destination is absolute fully specified path.
+    os.mkdir(destination)
+    full_filepath = os.path.join(destination, 'GRCh38_gencode_v26_CTAT_lib_Nov012017.plug-n-play.tar.gz')
+
+    #Download ref: https://dzone.com/articles/how-download-file-python
+    #f = urllib2.urlopen(ctat_resource_lib)
+    #data = f.read()
+    #with open(filepath, 'wb') as code:
+    #    code.write(data)
+
+    urllib.urlretrieve(url=ctat_resource_lib, filename=full_filepath)
+    # Put the following into a try statement, so that if there is a failure something can be printed about it before reraising exception.
+    tarfile.open(full_filepath, mode='r:*').extractall()
+    # FIX - There is additional processing that needs to happen for gmap-fusion to work.
+    # Get the root filename of the extracted file. 
+    # That directory is the actual destination that needs to be set as the ctat_genome_resource_library
+
+def main():
+    #Parse Command Line
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-d', '--download', action="store_true", \
+        help='Do not use if you already have the CTAT Resource Library that this program downloads.')
+    parser.add_argument('-g', '--genome_name', default="GRCh38_gencode_v26", \
+        help='Is used as the selector text of the entry in the data table.')
+    parser.add_argument('-p', '--destination_path', \
+        help='Full path of the CTAT Resource Library location or destination.')
+    parser.add_argument('-o', '--output_filename', \
+        help='Name of the output file, where the json dictionary will be written.')
+    args = parser.parse_args()
+
+    # All of the input parameters are written by default to the output file prior to
+    # this program being called.
+    # But I do not get input values from the json file, but rather from command line.
+    # Just leaving the following code as a comment, in case it might be useful to someone later.
+    # params = from_json_string(open(filename).read())
+    # target_directory = params['output_data'][0]['extra_files_path']
+    # os.mkdir(target_directory)
+
+    if args.download:
+        ctat_genome_resource_lib_path = download_from_BroadInst(destination=args.destination_path)
+    else:
+        # FIX - probably should check if this is a valid path with an actual CTAT Genome Ref Lib there.
+        ctat_genome_resource_lib_path = args.destination_path
+
+    if (args.genome_name is None) or (args.genome_name == ""):
+        genome_name = "GRCh38_gencode_v26"
+    else:
+        genome_name = args.genome_name
+
+    data_manager_dict = {}
+    data_manager_dict['data_tables'] = {}
+    data_manager_dict['data_tables']['ctat_genome_ref_libs'] = []
+    data_table_entry = dict(value="CTAT_RESOURCE_LIB", name=genome_name, path=ctat_genome_resource_lib_path)
+    data_manager_dict['data_tables']['ctat_genome_ref_libs'].append(data_table_entry)
+
+    # Save info to json file. This is used to transfer data from the DataManager tool, to the data manager,
+    # which then puts it into the correct .loc file (I think).
+    open(args.output_filename, 'wb').write(to_json_string(data_manager_dict))
+
+if __name__ == "__main__":
+    main()
+