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[project @ Allow user to provide FC##### to download or a path to a config file.]
author
Brandon King
<kingb@caltech.edu>
Fri, 30 Nov 2007 23:37:26 +0000
(23:37 +0000)
committer
Brandon King
<kingb@caltech.edu>
Fri, 30 Nov 2007 23:37:26 +0000
(23:37 +0000)
scripts/configure_pipeline
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diff --git
a/scripts/configure_pipeline
b/scripts/configure_pipeline
index d0d8b99af6cb36e37bedbb8eba746444e7220064..62ebb9b862192f2c79d0f797c25c3829a123c0f9 100644
(file)
--- a/
scripts/configure_pipeline
+++ b/
scripts/configure_pipeline
@@
-1,9
+1,16
@@
#!/usr/bin/env python
import os
import sys
#!/usr/bin/env python
import os
import sys
+import re
from gaworkflow.pipeline.configure_run import *
from gaworkflow.pipeline.monitors import startCmdLineStatusMonitor
from gaworkflow.pipeline.configure_run import *
from gaworkflow.pipeline.monitors import startCmdLineStatusMonitor
+s_fc = re.compile('FC[0-9]+')
+
+
+GENOME_DIR = '/data-store01/compbio/genomes/'
+
+
def main(args=None):
ci = ConfigInfo()
def main(args=None):
ci = ConfigInfo()
@@
-11,13
+18,24
@@
def main(args=None):
#FIXME: make a better command line tool
skip_retrieve_config = False
if len(args) == 1:
#FIXME: make a better command line tool
skip_retrieve_config = False
if len(args) == 1:
- cfg_filepath = os.path.abspath(args[0])
- skip_retrieve_config = True
+ arg = args[0]
+
+ #If FC##### found
+ if s_fc.search(arg):
+ cfg_filepath = os.path.abspath('config32auto.txt')
+ flowcell = arg
+ #else, config file provide
+ else:
+ cfg_filepath = os.path.abspath(args[0])
+ skip_retrieve_config = True
else:
else:
- cfg_filepath = os.path.abspath('config32auto.txt')
+ print "usage:\n" \
+ " configure_pipeline FC#####\n" \
+ " or:\n" \
+ " configure_pipeline <conf_filepath>\n"
+ return 3
- flowcell = 'FC12150'
- genome_dir = '/home/king/trog_drive/'
+ genome_dir = GENOME_DIR
if not skip_retrieve_config:
status_retrieve_cfg = retrieve_config(ci, flowcell, cfg_filepath, genome_dir)
if not skip_retrieve_config:
status_retrieve_cfg = retrieve_config(ci, flowcell, cfg_filepath, genome_dir)