opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Make the PBS script/stdout/stderr directory configurable.

Browse Source
This commit is contained in:
Nate Coraor
2009-01-09 17:08:49 -05:00
parent 1423af2fd5
commit 2f0f2dfb9a
3 changed files with 19 additions and 11 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/config.py
+2 -1
View File
@@ -44,6 +44,7 @@ class Configuration( object ):
self.cluster_job_queue_workers = int( kwargs.get( "cluster_job_queue_workers", "5" ) )
self.job_scheduler_policy = kwargs.get("job_scheduler_policy", "FIFO")
self.job_queue_cleanup_interval = int( kwargs.get("job_queue_cleanup_interval", "5") )
self.cluster_files_directory = resolve_path( kwargs.get( "cluster_files_directory", "database/pbs" ), self.root )
self.job_working_directory = resolve_path( kwargs.get( "job_working_directory", "database/job_working_directory" ), self.root )
self.outputs_to_working_directory = string_as_bool( kwargs.get( 'outputs_to_working_directory', False ) )
self.admin_pass = kwargs.get('admin_pass',"galaxy")
@@ -94,7 +95,7 @@ class Configuration( object ):
return default
def check( self ):
# Check that required directories exist
for path in self.root, self.file_path, self.tool_path, self.tool_data_path, self.template_path, self.job_working_directory:
for path in self.root, self.file_path, self.tool_path, self.tool_data_path, self.template_path, self.job_working_directory, self.cluster_files_directory:
if not os.path.isdir( path ):
raise ConfigurationError("Directory does not exist: %s" % path )
# Check that required files exist
lib/galaxy/jobs/__init__.py
+11 -4
View File
@@ -1,4 +1,4 @@
import logging, threading, sys, os, time, subprocess, string, tempfile, re, traceback
import logging, threading, sys, os, time, subprocess, string, tempfile, re, traceback, shutil
from galaxy import util, model
from galaxy.model import mapping
@@ -396,6 +396,13 @@ class JobWrapper( object ):
# if the job was deleted, don't fail it
if not job.state == model.Job.states.DELETED:
for dataset_assoc in job.output_datasets:
if self.app.config.outputs_to_working_directory:
false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % dataset_assoc.dataset.id ) )
if os.path.exists( false_path ):
shutil.move( false_path, dataset_assoc.dataset.file_name )
log.debug( "fail(): Moved %s to %s" % ( false_path, dataset_assoc.dataset.file_name ) )
else:
log.warning( "fail(): Missing output file in working directory: %s" % false_path )
dataset = dataset_assoc.dataset
dataset.refresh()
dataset.state = dataset.states.ERROR
@@ -474,10 +481,10 @@ class JobWrapper( object ):
if self.app.config.outputs_to_working_directory:
false_path = os.path.abspath( os.path.join( self.working_directory, "galaxy_dataset_%d.dat" % dataset_assoc.dataset.id ) )
if os.path.exists( false_path ):
os.rename( false_path, dataset_assoc.dataset.file_name )
log.debug( "Moved %s to %s" % ( false_path, dataset_assoc.dataset.file_name ) )
shutil.move( false_path, dataset_assoc.dataset.file_name )
log.debug( "finish(): Moved %s to %s" % ( false_path, dataset_assoc.dataset.file_name ) )
else:
log.warning( "Missing output file in working directory: %s" % false_path )
log.warning( "finish(): Missing output file in working directory: %s" % false_path )
for dataset in dataset_assoc.dataset.dataset.history_associations: #need to update all associated output hdas, i.e. history was shared with job running
dataset.blurb = 'done'
dataset.peek = 'no peek'
lib/galaxy/jobs/runners/pbs.py
+6 -6
View File
@@ -166,8 +166,8 @@ class PBSJobRunner( object ):
raise Exception( "Connection to PBS server for submit failed" )
# define job attributes
ofile = "%s/database/pbs/%s.o" % (os.getcwd(), job_wrapper.job_id)
efile = "%s/database/pbs/%s.e" % (os.getcwd(), job_wrapper.job_id)
ofile = "%s/%s.o" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
# If an application server is set, we're staging
if self.app.config.pbs_application_server:
@@ -201,7 +201,7 @@ class PBSJobRunner( object ):
script = pbs_symlink_template % (job_wrapper.galaxy_lib_dir, " ".join(job_wrapper.get_input_fnames() + job_wrapper.get_output_fnames()), self.app.config.pbs_stage_path, exec_dir, command_line)
else:
script = pbs_template % (job_wrapper.galaxy_lib_dir, exec_dir, command_line)
job_file = "%s/database/pbs/%s.sh" % (os.getcwd(), job_wrapper.job_id)
job_file = "%s/%s.sh" % (self.app.config.cluster_files_directory, job_wrapper.job_id)
fh = file(job_file, "w")
fh.write(script)
fh.close()
@@ -436,9 +436,9 @@ class PBSJobRunner( object ):
def recover( self, job, job_wrapper ):
"""Recovers jobs stuck in the queued/running state when Galaxy started"""
pbs_job_state = PBSJobState()
pbs_job_state.ofile = "%s/database/pbs/%s.o" % (os.getcwd(), job.id)
pbs_job_state.efile = "%s/database/pbs/%s.e" % (os.getcwd(), job.id)
pbs_job_state.job_file = "%s/database/pbs/%s.sh" % (os.getcwd(), job.id)
pbs_job_state.ofile = "%s/%s.o" % (self.app.config.cluster_files_directory, job.id)
pbs_job_state.efile = "%s/%s.e" % (self.app.config.cluster_files_directory, job.id)
pbs_job_state.job_file = "%s/%s.sh" % (self.app.config.cluster_files_directory, job.id)
pbs_job_state.job_id = str( job.job_runner_external_id )
pbs_job_state.runner_url = job_wrapper.tool.job_runner
job_wrapper.command_line = job.command_line