Commit d6726287 authored by RyanHerb's avatar RyanHerb

task.py defs.py.sample DIR_PEAR

Currently PEAR must be installed in a specific directory in order to be
executed during pre-processes.
Therefore adding a DIR_PEAR to the defs.py file will allow users to
reference existing PEAR installations without the need for adding
symbolic links to the vidjil installation.
parent 67918760
......@@ -688,7 +688,7 @@ def run_pre_process(pre_process_id, sequence_file_id, clean_before=True, clean_a
pre_process = db.pre_process[pre_process_id]
cmd = pre_process.command.replace( "&file1&", defs.DIR_SEQUENCES + sequence_file.data_file)
cmd = 'python ' + defs.DIR_PEAR + pre_process.command.replace( "&file1&", defs.DIR_SEQUENCES + sequence_file.data_file)
if sequence_file.data_file2:
cmd = cmd.replace( "&file2&", defs.DIR_SEQUENCES + sequence_file.data_file2)
cmd = cmd.replace( "&result&", output_file)
......
......@@ -39,6 +39,7 @@ BASENAME_OUT_VIDJIL_ID = '%06d'
DIR_VIDJIL = '../../'
DIR_FUSE = '../../tools'
DIR_MIXCR = '../../'
DIR_PEAR = '../../'
### Directory that store the germlines used by Vidjil
DIR_GERMLINE = DIR_VIDJIL + 'germline/'
......
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