From 385d5f5223e9da95c150a3a8fef1bc69ae1a6fe4 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Fri, 31 Aug 2012 19:53:03 -0700 Subject: [PATCH] Automatically add the flowcell subdirectory to the sequence archive path --- encode_submission/geo_gather.py | 3 ++- encode_submission/ucsc_gather.py | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) 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) -- 2.30.2