details: http://www.bx.psu.edu/hg/galaxy/rev/b6252802e0b6 changeset: 3164:b6252802e0b6 user: Greg Von Kuster greg@bx.psu.edu date: Wed Dec 09 15:21:41 2009 -0500 description: Fix gencode partition tool to not use hard-coded paths.
diffstat:
tools/encode/gencode_partition.xml | 2 +- tools/encode/split_by_partitions.py | 5 +++-- 2 files changed, 4 insertions(+), 3 deletions(-)
diffs (26 lines):
diff -r f93272d4a4a1 -r b6252802e0b6 tools/encode/gencode_partition.xml --- a/tools/encode/gencode_partition.xml Wed Dec 09 13:15:33 2009 -0500 +++ b/tools/encode/gencode_partition.xml Wed Dec 09 15:21:41 2009 -0500 @@ -1,6 +1,6 @@ <tool id="gencode_partition1" name="Gencode Partition"> <description>an interval file</description> - <command interpreter="python">split_by_partitions.py /home/universe/encode_feature_partitions/partition_list.txt $input1 $out_file1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol}</command> + <command interpreter="python">split_by_partitions.py ${GALAXY_DATA_INDEX_DIR} $input1 $out_file1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol}</command> <inputs> <param name="input1" type="data" format="interval" label="File to Partition"/> </inputs> diff -r f93272d4a4a1 -r b6252802e0b6 tools/encode/split_by_partitions.py --- a/tools/encode/split_by_partitions.py Wed Dec 09 13:15:33 2009 -0500 +++ b/tools/encode/split_by_partitions.py Wed Dec 09 15:21:41 2009 -0500 @@ -18,8 +18,9 @@ sys.exit()
def main(): - partition_index = sys.argv[1] - partition_offset = "/home/universe/encode_feature_partitions/" #should parse perhaps from index filepath + GALAXY_DATA_INDEX_DIR = sys.argv[1] + partition_index = '%s/encode_feature_partitions/partition_list.txt' % GALAXY_DATA_INDEX_DIR + partition_offset = "%s/encode_feature_partitions/" % GALAXY_DATA_INDEX_DIR
warnings = []