Commit f2ec1071 authored by fabrice's avatar fabrice
Browse files

Removed working directory path in .ini file. ariaproject now generated using...

Removed working directory path in .ini file. ariaproject now generated using outdir command line arg
parent 082a3694
No preview for this file type
No preview for this file type
No preview for this file type
...@@ -73,7 +73,6 @@ nd_control: 0 ...@@ -73,7 +73,6 @@ nd_control: 0
runid: 1 runid: 1
cpus: 100 cpus: 100
host_command: sbatch --cores-per-socket=10 -o /baycells/home/fallain/slurm.errors host_command: sbatch --cores-per-socket=10 -o /baycells/home/fallain/slurm.errors
working_directory: data/examples/out/setup
temp_root: data/examples/out/setup temp_root: data/examples/out/setup
parameter_definition: automatic parameter_definition: automatic
ss_dist_format: tbl ss_dist_format: tbl
......
...@@ -712,6 +712,15 @@ class AriaEcXMLConverter(AriaXMLConverter): ...@@ -712,6 +712,15 @@ class AriaEcXMLConverter(AriaXMLConverter):
def write_ariaproject(self, aria_template, seqfile, dist_files, tbl_files, def write_ariaproject(self, aria_template, seqfile, dist_files, tbl_files,
desc=""): desc=""):
"""
Generate ariaproject.xml file
:param aria_template: ariaproject.xml template path
:param seqfile:
:param dist_files:
:param tbl_files:
:param desc:
:return:
"""
if aria_template: if aria_template:
template = os.path.abspath(aria_template) template = os.path.abspath(aria_template)
...@@ -737,26 +746,24 @@ class AriaEcXMLConverter(AriaXMLConverter): ...@@ -737,26 +746,24 @@ class AriaEcXMLConverter(AriaXMLConverter):
'the ratio %.2f:%.2f' % (steps_1, steps_2)) 'the ratio %.2f:%.2f' % (steps_1, steps_2))
aria_project_dict.update(self.settings.setup.config) aria_project_dict.update(self.settings.setup.config)
work_dir = os.path.abspath(aria_project_dict['working_directory']) work_dir = os.path.abspath(self.settings.outdir)
temp_root = os.path.abspath(aria_project_dict['temp_root']) temp_root = os.path.abspath(aria_project_dict['temp_root'])
if not os.path.exists(work_dir) or not os.path.exists(temp_root): if not os.path.exists(work_dir) or not os.path.exists(temp_root):
logger.info("Working dir %s and temp directory %s doesn't exist." % ( logger.info("Working dir %s doesn't exist." % work_dir)
work_dir, temp_root))
logger.info("Create new directory %s" % work_dir) logger.info("Create new directory %s" % work_dir)
os.makedirs(work_dir) os.makedirs(work_dir)
if not os.path.exists(temp_root):
logger.info("Temp directory %s doesn't exist." % temp_root)
logger.info("Create new directory %s" % temp_root) logger.info("Create new directory %s" % temp_root)
os.makedirs(temp_root) os.makedirs(temp_root)
for direct in (work_dir, temp_root): if not os.path.exists(os.path.join(temp_root, self.outprefix)):
os.makedirs(os.path.join(temp_root, self.outprefix))
if not os.path.exists(os.path.join(direct, self.outprefix)): if not os.path.exists(os.path.join(temp_root, self.outprefix, desc)):
os.makedirs(os.path.join(direct, self.outprefix)) os.makedirs(os.path.join(temp_root, self.outprefix, desc))
if not os.path.exists(os.path.join(direct, self.outprefix, desc)):
os.makedirs(os.path.join(direct, self.outprefix, desc))
work_dir = os.path.join(work_dir, self.outprefix, desc)
temp_root = os.path.join(temp_root, self.outprefix, desc) temp_root = os.path.join(temp_root, self.outprefix, desc)
aria_project_dict['working_directory'] = work_dir aria_project_dict['working_directory'] = work_dir
......
No preview for this file type
No preview for this file type
No preview for this file type
No preview for this file type
No preview for this file type
No preview for this file type
No preview for this file type
# Do not edit this file, pipeline versioning is governed by git tags # Do not edit this file, pipeline versioning is governed by git tags
__version__=v0.1.11-dev1 __version__=v0.1.11-dev2
\ No newline at end of file \ No newline at end of file
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment