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Set WITH_SEQUENCE as both a per-lane AND global parameter
[htsworkflow.git]
/
htsworkflow
/
pipelines
/
retrieve_config.py
diff --git
a/htsworkflow/pipelines/retrieve_config.py
b/htsworkflow/pipelines/retrieve_config.py
index 136bb5a50c60ff8890a35b6b579426ca6f593257..3a1a56aeaf2188350db8b980d7b098bf0098a0ba 100644
(file)
--- a/
htsworkflow/pipelines/retrieve_config.py
+++ b/
htsworkflow/pipelines/retrieve_config.py
@@
-14,6
+14,7
@@
except ImportError, e:
import simplejson as json
from htsworkflow.frontend.auth import apidata
import simplejson as json
from htsworkflow.frontend.auth import apidata
+from htsworkflow.util import api
from htsworkflow.util.url import normalize_url
from htsworkflow.pipelines.genome_mapper import getAvailableGenomes
from htsworkflow.pipelines.genome_mapper import constructMapperDict
from htsworkflow.util.url import normalize_url
from htsworkflow.pipelines.genome_mapper import getAvailableGenomes
from htsworkflow.pipelines.genome_mapper import constructMapperDict
@@
-36,7
+37,7
@@
def retrieve_flowcell_info(base_host_url, flowcell):
"""
Return a dictionary describing a
"""
"""
Return a dictionary describing a
"""
- url =
base_host_url + '/experiments/config/%s/json' % (
flowcell)
+ url =
api.flowcell_url(base_host_url,
flowcell)
try:
apipayload = urllib.urlencode(apidata)
try:
apipayload = urllib.urlencode(apidata)
@@
-107,7
+108,6
@@
def format_gerald_header(flowcell_info):
config += ['Lane%s: %s | %s' % (lane_number, lane_info['library_id'],
lane_info['library_name'])]
config += ['Lane%s: %s | %s' % (lane_number, lane_info['library_id'],
lane_info['library_name'])]
- config += ['SEQUENCE_FORMAT --fastq']
config += ['']
return "\n# ".join(config)
config += ['']
return "\n# ".join(config)
@@
-123,6
+123,10
@@
def format_gerald_config(options, flowcell_info, genome_map):
# in the config file... things like which lane is which library.
config = [format_gerald_header(flowcell_info)]
# in the config file... things like which lane is which library.
config = [format_gerald_header(flowcell_info)]
+ config += ['SEQUENCE_FORMAT --fastq']
+ config += ['ELAND_SET_SIZE 20']
+ config += ['WITH_SEQUENCE TRUE']
+ config += ['12345678:WITH_SEQUENCE TRUE']
analysis_suffix = eland_analysis_suffix[flowcell_info['paired_end']]
sequence_suffix = sequence_analysis_suffix[flowcell_info['paired_end']]
lane_groups = group_lane_parameters(flowcell_info)
analysis_suffix = eland_analysis_suffix[flowcell_info['paired_end']]
sequence_suffix = sequence_analysis_suffix[flowcell_info['paired_end']]
lane_groups = group_lane_parameters(flowcell_info)
@@
-140,7
+144,7
@@
def format_gerald_config(options, flowcell_info, genome_map):
is_sequencing = True
if is_sequencing:
is_sequencing = True
if is_sequencing:
- config += ['%s:ANALYSIS sequence%s' % (lane_prefix,
analysis
_suffix)]
+ config += ['%s:ANALYSIS sequence%s' % (lane_prefix,
sequence
_suffix)]
else:
config += ['%s:ANALYSIS eland%s' % (lane_prefix, analysis_suffix)]
config += ['%s:ELAND_GENOME %s' % (lane_prefix, species_path) ]
else:
config += ['%s:ANALYSIS eland%s' % (lane_prefix, analysis_suffix)]
config += ['%s:ELAND_GENOME %s' % (lane_prefix, species_path) ]
@@
-148,8
+152,9
@@
def format_gerald_config(options, flowcell_info, genome_map):
config += ['%s:USE_BASES Y%s' % ( lane_prefix, read_length ) ]
# add in option for running script after
config += ['%s:USE_BASES Y%s' % ( lane_prefix, read_length ) ]
# add in option for running script after
- if options.post_run is not None:
- post_run = options.post_run % {'runfolder': options.runfolder}
+ if not (options.post_run is None or options.runfolder is None):
+ runfolder = os.path.abspath(options.runfolder)
+ post_run = options.post_run % {'runfolder': runfolder}
config += ['POST_RUN_COMMAND %s' % (post_run,) ]
config += [''] # force trailing newline
config += ['POST_RUN_COMMAND %s' % (post_run,) ]
config += [''] # force trailing newline
@@
-203,8
+208,9
@@
Config File:
Example Config File:
[%s]
Example Config File:
[%s]
- config_host=http://somewhere.domain:port
- genome_dir=/path to search for genomes
+ config_host: http://somewhere.domain:port
+ genome_dir: /path to search for genomes
+ post_run: runfolder -o <destdir> %%(runfolder)s
""" % (CONFIG_SYSTEM, CONFIG_USER, GERALD_CONFIG_SECTION)
""" % (CONFIG_SYSTEM, CONFIG_USER, GERALD_CONFIG_SECTION)