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Fix gencode partition tool to not use hard-coded paths.

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This commit is contained in:
Greg Von Kuster
2009-12-09 15:21:41 -05:00
parent 7bcfda8b9c
commit 4071d88e5c
2 changed files with 4 additions and 3 deletions
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tools/encode/gencode_partition.xml
+1 -1
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@@ -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>
tools/encode/split_by_partitions.py
+3 -2
View File
@@ -18,8 +18,9 @@ def stop_err( msg ):
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 = []