From: Diane Trout <diane@caltech.edu>
Date: Sat, 1 Sep 2012 02:53:03 +0000 (-0700)
Subject: Automatically add the flowcell subdirectory to the sequence archive path
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=385d5f5223e9da95c150a3a8fef1bc69ae1a6fe4

Automatically add the flowcell subdirectory to the sequence archive path
---

diff --git a/encode_submission/geo_gather.py b/encode_submission/geo_gather.py
index 9a1f51e..a290105 100644
--- a/encode_submission/geo_gather.py
+++ b/encode_submission/geo_gather.py
@@ -77,7 +77,8 @@ def main(cmdline=None):
         results.make_tree_from(opts.make_tree_from)
 
     if opts.fastq:
-        extractor = CondorFastqExtract(opts.host, apidata, opts.sequence,
+        flowcells = os.path.join(opts.sequence, 'flowcells')
+        extractor = CondorFastqExtract(opts.host, flowcells,
                                        force=opts.force)
         extractor.create_scripts(results)
 
diff --git a/encode_submission/ucsc_gather.py b/encode_submission/ucsc_gather.py
index 811ffdf..a9fa72a 100644
--- a/encode_submission/ucsc_gather.py
+++ b/encode_submission/ucsc_gather.py
@@ -96,7 +96,8 @@ def main(cmdline=None):
         mapper.link_daf(results)
 
     if opts.fastq:
-        extractor = CondorFastqExtract(opts.host, apidata, opts.sequence,
+        flowcells = os.path.join(opts.sequence, 'flowcells')
+        extractor = CondorFastqExtract(opts.host, flowcells,
                                        force=opts.force)
         extractor.create_scripts(results)