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.

server/web2py/applications/vidjil/models/task.py

@@ -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)

server/web2py/applications/vidjil/modules/defs.py.sample

@@ -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/'