# HG changeset patch
# User sanbi-uwc
# Date 1454919814 18000
# Node ID 2883a3b7dc56e346d9db5c6ced0bac5dcedbef4b
planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
diff -r 000000000000 -r 2883a3b7dc56 data_manager/rnastar_index_builder.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/rnastar_index_builder.py Mon Feb 08 03:23:34 2016 -0500
@@ -0,0 +1,71 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+import argparse
+from subprocess import check_call, CalledProcessError
+from json import load, dump
+from os import environ, mkdir
+from os.path import isdir, exists
+import shlex
+import sys
+
+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 make_rnastar_index(output_directory, fasta_filename):
+# STAR
+# --runMode genomeGenerate
+# --genomeDir tempstargenomedir
+# --genomeFastaFiles $input1
+# --runThreadsN \${GALAXY_SLOTS:-1}
+# --genomeChrBinNbits $advanced_options.chr_bin_nbits
+
+ if exists(output_directory) and not isdir(output_directory):
+ print("Output directory path already exists but is not a directory: {}".format(output_directory), file=sys.stderr)
+ elif not exists(output_directory):
+ mkdir(output_directory)
+
+ if 'GALAXY_SLOTS' in environ:
+ nslots = environ['GALAXY_SLOTS']
+ else:
+ nslots = 1
+
+ # cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadsN {}'.format(output_directory,
+ # fasta_filename,
+ # nslots)
+ # cmdline = shlex.split(cmdline_str)
+ cmdline = ('touch', '{}/foo'.format(output_directory))
+ try:
+ check_call(cmdline)
+ except CalledProcessError:
+ print("Error building RNA STAR index", file=sys.stderr)
+ return(output_directory)
+
+parser = argparse.ArgumentParser(description="Generate RNA STAR genome index and JSON describing this")
+parser.add_argument('output_filename')
+parser.add_argument('--fasta_filename')
+parser.add_argument('--fasta_dbkey')
+parser.add_argument('--fasta_description', default=None)
+parser.add_argument('--data_table_name', default='rnastar_indexes')
+args = parser.parse_args()
+
+params = load(open(args.output_filename, 'rb'))
+
+output_directory = params['output_data'][0]['extra_files_path']
+
+make_rnastar_index(output_directory, args.fasta_filename)
+(sequence_id, sequence_name) = get_id_name(params, args.fasta_dbkey, args.fasta_description)
+data_table_entry = dict(value=sequence_id, dbkey=args.fasta_dbkey, name=sequence_name, path=output_directory)
+output_datatable_dict = dict('data_tables', dict(args.data_table_name, [data_table_entry]))
+
+dump(output_datatable_dict(open(args.output_file, 'wb')))
\ No newline at end of file
diff -r 000000000000 -r 2883a3b7dc56 data_manager/rnastar_index_builder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/rnastar_index_builder.xml Mon Feb 08 03:23:34 2016 -0500
@@ -0,0 +1,34 @@
+
+
+ Build an index for use by the RNA STAR mapping tool
+
+ rnastar
+
+ bwa_index_builder.py "${out_file}" --fasta_filename "${input1.fields.path}" --fasta_dbkey "${input1.fields.dbkey}" --fasta_description "${input1.fields.name}" --data_table_name "rnastar_indexes"
+
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+
+ Help!
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+
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diff -r 000000000000 -r 2883a3b7dc56 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Mon Feb 08 03:23:34 2016 -0500
@@ -0,0 +1,17 @@
+
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+ ${dbkey}/rnastar_index/${value}
+
+ ${GALAXY_DATA_MANAGER_DATA_PATH}/{$dbkey}/rnastar_index/${value}/${path}
+ abspath
+
+
+
+
\ No newline at end of file
diff -r 000000000000 -r 2883a3b7dc56 tool-data/rnastar_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/rnastar_indexes.loc.sample Mon Feb 08 03:23:34 2016 -0500
@@ -0,0 +1,2 @@
+#TODO: Document
+#
diff -r 000000000000 -r 2883a3b7dc56 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Mon Feb 08 03:23:34 2016 -0500
@@ -0,0 +1,10 @@
+
+
+
+
+
+ Installs the STAR wrapper and dependency package star - see https://github.com/alexdobin/STAR
+ STAR is a very fast mapper for rna-seq giving junctions if the indexes are constructed with a junction library
+
+
+