1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/07bc7e9dd794/
changeset: r5055:07bc7e9dd794
user: jgoecks
date: 2011-02-14 19:21:04
summary: Fix bug in extract_genomic_dna.py so that comment lines are correctly handled.
affected #: 1 file (43 bytes)
--- a/tools/extract/extract_genomic_dna.py Mon Feb 14 10:56:06 2011 -0500
+++ b/tools/extract/extract_genomic_dna.py Mon Feb 14 13:21:04 2011 -0500
@@ -162,6 +162,8 @@
if strand not in ['+', '-']:
strand = '+'
sequence = ''
+ else:
+ continue
# Open sequence file and get sequence for feature/interval.
if seq_path and os.path.exists( "%s/%s.nib" % ( seq_path, chrom ) ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/1c184746177e/
changeset: r5054:1c184746177e
user: natefoo
date: 2011-02-14 16:56:06
summary: Fix for PBS job runner importing itself instead of pbs_python.
affected #: 1 file (15 bytes)
--- a/lib/galaxy/jobs/runners/pbs.py Mon Feb 14 09:08:04 2011 -0500
+++ b/lib/galaxy/jobs/runners/pbs.py Mon Feb 14 10:56:06 2011 -0500
@@ -25,7 +25,7 @@
try:
pkg_resources.require( "pbs_python" )
- import pbs
+ pbs = __import__( "pbs" )
except Exception, e:
raise Exception( egg_message % str( e ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/f3e91f8ea422/
changeset: r5053:f3e91f8ea422
user: natefoo
date: 2011-02-14 15:08:04
summary: Fix infinite loop setting up locales.
affected #: 1 file (14 bytes)
--- a/lib/galaxy/web/framework/__init__.py Fri Feb 11 16:55:14 2011 -0500
+++ b/lib/galaxy/web/framework/__init__.py Mon Feb 14 09:08:04 2011 -0500
@@ -201,8 +201,8 @@
locales = []
if 'HTTP_ACCEPT_LANGUAGE' in self.environ:
# locales looks something like: ['en', 'en-us;q=0.7', 'ja;q=0.3']
- locales = self.environ['HTTP_ACCEPT_LANGUAGE'].split( ',' )
- for locale in locales:
+ client_locales = self.environ['HTTP_ACCEPT_LANGUAGE'].split( ',' )
+ for locale in client_locales:
try:
locales.append( Locale.parse( locale.split( ';' )[0], sep='-' ).language )
except UnknownLocaleError:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/2b7295ac12dc/
changeset: r5051:2b7295ac12dc
user: natefoo
date: 2011-02-11 22:15:18
summary: Instead of raising in exception, default to english if a locale is set by the client but not installed on the server.
affected #: 1 file (177 bytes)
--- a/lib/galaxy/web/framework/__init__.py Fri Feb 11 15:32:13 2011 -0500
+++ b/lib/galaxy/web/framework/__init__.py Fri Feb 11 16:15:18 2011 -0500
@@ -27,7 +27,7 @@
pkg_resources.require( "Babel" )
from babel.support import Translations
-from babel import Locale
+from babel import Locale, UnknownLocaleError
pkg_resources.require( "SQLAlchemy >= 0.4" )
from sqlalchemy import and_
@@ -198,11 +198,16 @@
# and such).
self.workflow_building_mode = False
def setup_i18n( self ):
+ locales = []
if 'HTTP_ACCEPT_LANGUAGE' in self.environ:
# locales looks something like: ['en', 'en-us;q=0.7', 'ja;q=0.3']
locales = self.environ['HTTP_ACCEPT_LANGUAGE'].split( ',' )
- locales = [ Locale.parse(l.split( ';' )[0], sep='-').language for l in locales ]
- else:
+ for locale in locales:
+ try:
+ locales.append( Locale.parse( locale.split( ';' )[0], sep='-' ).language )
+ except UnknownLocaleError:
+ pass
+ if not locales:
# Default to English
locales = 'en'
t = Translations.load( dirname='locale', locales=locales, domain='ginga' )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/a5846ac40596/
changeset: r5049:a5846ac40596
user: natefoo
date: 2011-02-11 21:01:04
summary: Handle bugs encountered when fetching an egg during a version conflict and a sys.path item has been removed.
affected #: 1 file (939 bytes)
--- a/lib/galaxy/eggs/__init__.py Fri Feb 11 14:17:22 2011 -0500
+++ b/lib/galaxy/eggs/__init__.py Fri Feb 11 15:01:04 2011 -0500
@@ -45,6 +45,7 @@
self.crate = crate
self.distribution = None
self.dir = None
+ self.removed_location = None
if self.name is not None and self.version is not None:
self.set_distribution()
def set_dir( self ):
@@ -103,34 +104,50 @@
pkg_resources.compatible_platforms( tmp_dist.platform, pkg_resources.get_platform() ):
return file
return None
- if self.url is None:
- return None
- alternative = None
- try:
- url = self.url + '/' + self.distribution.egg_name() + '.egg'
- URLRetriever().retrieve( url, self.distribution.location )
- log.debug( "Fetched %s" % url )
- except IOError, e:
- if e[1] == 404 and self.distribution.platform != py:
- alternative = find_alternative()
- if alternative is None:
- return None
- else:
- return None
- if alternative is not None:
+ def _fetch():
+ if self.url is None:
+ return False
+ alternative = None
try:
- url = '/'.join( ( self.url, alternative ) )
- URLRetriever().retrieve( url, os.path.join( self.dir, alternative ) )
+ url = self.url + '/' + self.distribution.egg_name() + '.egg'
+ URLRetriever().retrieve( url, self.distribution.location )
log.debug( "Fetched %s" % url )
except IOError, e:
- return None
- self.platform = alternative.split( '-', 2 )[-1].rsplit( '.egg', 1 )[0]
- self.set_distribution()
- self.unpack_if_needed()
- self.remove_doppelgangers()
- global env
- env = get_env() # reset the global Environment object now that we've obtained a new egg
- return self.distribution
+ if e[1] == 404 and self.distribution.platform != py:
+ alternative = find_alternative()
+ if alternative is None:
+ return False
+ else:
+ return False
+ if alternative is not None:
+ try:
+ url = '/'.join( ( self.url, alternative ) )
+ URLRetriever().retrieve( url, os.path.join( self.dir, alternative ) )
+ log.debug( "Fetched %s" % url )
+ except IOError, e:
+ return False
+ self.platform = alternative.split( '-', 2 )[-1].rsplit( '.egg', 1 )[0]
+ self.set_distribution()
+ self.unpack_if_needed()
+ self.remove_doppelgangers()
+ return True
+ # If being called from a version conflict, that code has removed a
+ # directory from sys.path. That directory could be Python's main lib
+ # directory (e.g. in the case of wsgiref under 2.6). Temporarily put
+ # it back during the execution of this code.
+ if self.removed_location:
+ sys.path.append( self.removed_location )
+ try:
+ assert _fetch()
+ rval = self.distribution
+ except:
+ rval = None
+ if self.removed_location:
+ sys.path.remove( self.removed_location )
+ if rval is not None:
+ global env
+ env = get_env() # reset the global Environment object now that we've obtained a new egg
+ return rval
def unpack_if_needed( self ):
meta = pkg_resources.EggMetadata( zipimport.zipimporter( self.distribution.location ) )
if meta.has_metadata( 'not-zip-safe' ):
@@ -200,7 +217,10 @@
sys.path.remove(entry)
# if the conflict is a dpeendent egg, fetch that specific egg
if egg:
+ # Store the removed path so the fetch method can use it
+ egg.removed_location = location
r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch )
+ egg.removed_location = None
else:
r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env )
# re-add the path if it's a non-egg dir, in case more deps live there
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/4397e753ec2c/
changeset: r5048:4397e753ec2c
user: natefoo
date: 2011-02-11 20:17:22
summary: Fix a minor bug which mad it completely impossible to run a job.
affected #: 1 file (1 byte)
--- a/lib/galaxy/jobs/__init__.py Fri Feb 11 13:12:27 2011 -0500
+++ b/lib/galaxy/jobs/__init__.py Fri Feb 11 14:17:22 2011 -0500
@@ -1033,7 +1033,7 @@
for obj in module.__all__:
display_name = ':'.join( ( module_name, obj ) )
runner = getattr( module, obj )
- self.job_runners[obj] = runner( self.app )
+ self.job_runners[name] = runner( self.app )
log.debug( 'Loaded job runner: %s' % display_name )
def put( self, job_wrapper ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/6937b1a3b3a2/
changeset: r5047:6937b1a3b3a2
user: natefoo
date: 2011-02-11 19:12:27
summary: Make loading of job runners dynamic. Changes to lib/galaxy/config.py and lib/galaxy/jobs/__init__.py are no longer required. Existing runners which are not part of the Galaxy source will need to define the class name to instantiate in the __all__ list in the runner. See the included runners for an example.
affected #: 7 files (2.2 KB)
--- a/lib/galaxy/config.py Fri Feb 11 09:27:10 2011 -0500
+++ b/lib/galaxy/config.py Fri Feb 11 13:12:27 2011 -0500
@@ -189,16 +189,6 @@
for path in self.tool_config, self.datatypes_config:
if not os.path.isfile(path):
raise ConfigurationError("File not found: %s" % path )
- # Check job runners so the admin can scramble dependent egg.
- if self.start_job_runners is not None:
- runner_to_egg = dict( pbs = 'pbs_python', sge = 'DRMAA_python', drmaa = 'drmaa' )
- for runner in self.start_job_runners.split( ',' ):
- try:
- pkg_resources.require( runner_to_egg[runner] )
- except eggs.EggNotFetchable, e:
- raise eggs.EggNotFetchable( 'You must scramble the %s egg to use the %s job runner. Instructions are available at:\n http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster' % ( runner_to_egg[runner], runner ) )
- except KeyError:
- raise Exception( 'No such job runner: %s. Please double-check the value of start_job_runners in universe_wsgi.ini' % runner )
# Check for deprecated options.
for key in self.config_dict.keys():
if key in self.deprecated_options:
--- a/lib/galaxy/jobs/__init__.py Fri Feb 11 09:27:10 2011 -0500
+++ b/lib/galaxy/jobs/__init__.py Fri Feb 11 13:12:27 2011 -0500
@@ -1015,44 +1015,58 @@
start_job_runners.extend( app.config.start_job_runners.split(",") )
if app.config.use_tasked_jobs:
start_job_runners.append("tasks")
- for runner_name in start_job_runners:
- if runner_name == "local":
- import runners.local
- self.job_runners[runner_name] = runners.local.LocalJobRunner( app )
- elif runner_name == "tasks":
- import runners.tasks
- self.job_runners[runner_name] = runners.tasks.TaskedJobRunner( app )
- elif runner_name == "pbs":
- import runners.pbs
- self.job_runners[runner_name] = runners.pbs.PBSJobRunner( app )
- elif runner_name == "sge":
- import runners.sge
- self.job_runners[runner_name] = runners.sge.SGEJobRunner( app )
- elif runner_name == "drmaa":
- import runners.drmaa
- self.job_runners[runner_name] = runners.drmaa.DRMAAJobRunner( app )
- else:
- log.error( "Unable to start unknown job runner: '%s'" %runner_name )
+ for name in start_job_runners:
+ self._load_plugin( name )
+
+ def _load_plugin( self, name ):
+ module_name = 'galaxy.jobs.runners.' + name
+ try:
+ module = __import__( module_name )
+ except:
+ log.exception( 'Job runner is not loadable: %s' % module_name )
+ return
+ for comp in module_name.split( "." )[1:]:
+ module = getattr( module, comp )
+ if '__all__' not in dir( module ):
+ log.error( 'Runner "%s" does not contain a list of exported classes in __all__' % module_name )
+ return
+ for obj in module.__all__:
+ display_name = ':'.join( ( module_name, obj ) )
+ runner = getattr( module, obj )
+ self.job_runners[obj] = runner( self.app )
+ log.debug( 'Loaded job runner: %s' % display_name )
def put( self, job_wrapper ):
- if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None and not isinstance(job_wrapper, TaskWrapper):
- runner_name = "tasks"
- log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) )
- self.job_runners[runner_name].put( job_wrapper )
- else:
- runner_name = ( job_wrapper.tool.job_runner.split(":", 1) )[0]
- log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) )
- self.job_runners[runner_name].put( job_wrapper )
+ try:
+ if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None and not isinstance(job_wrapper, TaskWrapper):
+ runner_name = "tasks"
+ log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) )
+ self.job_runners[runner_name].put( job_wrapper )
+ else:
+ runner_name = ( job_wrapper.tool.job_runner.split(":", 1) )[0]
+ log.debug( "dispatching job %d to %s runner" %( job_wrapper.job_id, runner_name ) )
+ self.job_runners[runner_name].put( job_wrapper )
+ except KeyError:
+ log.error( 'put(): (%s) Invalid job runner: %s' % ( job_wrapper.job_id, runner_name ) )
+ job_wrapper.fail( 'Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.' )
def stop( self, job ):
runner_name = ( job.job_runner_name.split(":", 1) )[0]
log.debug( "stopping job %d in %s runner" %( job.id, runner_name ) )
- self.job_runners[runner_name].stop_job( job )
+ try:
+ self.job_runners[runner_name].stop_job( job )
+ except KeyError:
+ log.error( 'stop(): (%s) Invalid job runner: %s' % ( job_wrapper.job_id, runner_name ) )
+ # Job and output dataset states have already been updated, so nothing is done here.
def recover( self, job, job_wrapper ):
runner_name = ( job.job_runner_name.split(":", 1) )[0]
log.debug( "recovering job %d in %s runner" %( job.id, runner_name ) )
- self.job_runners[runner_name].recover( job, job_wrapper )
+ try:
+ self.job_runners[runner_name].recover( job, job_wrapper )
+ except KeyError:
+ log.error( 'recover(): (%s) Invalid job runner: %s' % ( job_wrapper.job_id, runner_name ) )
+ job_wrapper.fail( 'Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.' )
def shutdown( self ):
for runner in self.job_runners.itervalues():
--- a/lib/galaxy/jobs/runners/drmaa.py Fri Feb 11 09:27:10 2011 -0500
+++ b/lib/galaxy/jobs/runners/drmaa.py Fri Feb 11 13:12:27 2011 -0500
@@ -8,29 +8,29 @@
import pkg_resources
-try:
- if sys.version_info[:2] == ( 2, 4 ):
- pkg_resources.require( "ctypes" )
- pkg_resources.require( "drmaa" )
- drmaa = __import__( "drmaa" )
-except Exception, e:
- drmaa = str( e )
+if sys.version_info[:2] == ( 2, 4 ):
+ pkg_resources.require( "ctypes" )
+pkg_resources.require( "drmaa" )
+# We foolishly named this file the same as the name exported by the drmaa
+# library... 'import drmaa' import itself.
+drmaa = __import__( "drmaa" )
log = logging.getLogger( __name__ )
-if type( drmaa ) != str:
- drmaa_state = {
- drmaa.JobState.UNDETERMINED: 'process status cannot be determined',
- drmaa.JobState.QUEUED_ACTIVE: 'job is queued and active',
- drmaa.JobState.SYSTEM_ON_HOLD: 'job is queued and in system hold',
- drmaa.JobState.USER_ON_HOLD: 'job is queued and in user hold',
- drmaa.JobState.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold',
- drmaa.JobState.RUNNING: 'job is running',
- drmaa.JobState.SYSTEM_SUSPENDED: 'job is system suspended',
- drmaa.JobState.USER_SUSPENDED: 'job is user suspended',
- drmaa.JobState.DONE: 'job finished normally',
- drmaa.JobState.FAILED: 'job finished, but failed',
- }
+__all__ = [ 'DRMAAJobRunner' ]
+
+drmaa_state = {
+ drmaa.JobState.UNDETERMINED: 'process status cannot be determined',
+ drmaa.JobState.QUEUED_ACTIVE: 'job is queued and active',
+ drmaa.JobState.SYSTEM_ON_HOLD: 'job is queued and in system hold',
+ drmaa.JobState.USER_ON_HOLD: 'job is queued and in user hold',
+ drmaa.JobState.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold',
+ drmaa.JobState.RUNNING: 'job is running',
+ drmaa.JobState.SYSTEM_SUSPENDED: 'job is system suspended',
+ drmaa.JobState.USER_SUSPENDED: 'job is user suspended',
+ drmaa.JobState.DONE: 'job finished normally',
+ drmaa.JobState.FAILED: 'job finished, but failed',
+}
drm_template = """#!/bin/sh
#$ -S /bin/sh
@@ -70,8 +70,6 @@
def __init__( self, app ):
"""Initialize this job runner and start the monitor thread"""
# Check if drmaa was importable, fail if not
- if type( drmaa ) == str:
- raise Exception( "DRMAAJobRunner requires drmaa module which could not be loaded: %s" % drmaa )
self.app = app
self.sa_session = app.model.context
# 'watched' and 'queue' are both used to keep track of jobs to watch.
--- a/lib/galaxy/jobs/runners/local.py Fri Feb 11 09:27:10 2011 -0500
+++ b/lib/galaxy/jobs/runners/local.py Fri Feb 11 13:12:27 2011 -0500
@@ -12,6 +12,8 @@
log = logging.getLogger( __name__ )
+__all__ = [ 'LocalJobRunner' ]
+
class LocalJobRunner( BaseJobRunner ):
"""
Job runner backed by a finite pool of worker threads. FIFO scheduling
--- a/lib/galaxy/jobs/runners/pbs.py Fri Feb 11 09:27:10 2011 -0500
+++ b/lib/galaxy/jobs/runners/pbs.py Fri Feb 11 13:12:27 2011 -0500
@@ -11,14 +11,28 @@
import pkg_resources
+egg_message = """
+
+The 'pbs' runner depends on 'pbs_python' which is not installed or not
+configured properly. Galaxy's "scramble" system should make this installation
+simple, please follow the instructions found at:
+
+ http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
+
+Additional errors may follow:
+%s
+"""
+
try:
pkg_resources.require( "pbs_python" )
- pbs = __import__( "pbs" )
-except:
- pbs = None
+ import pbs
+except Exception, e:
+ raise Exception( egg_message % str( e ) )
log = logging.getLogger( __name__ )
+__all__ = [ 'PBSJobRunner' ]
+
pbs_template = """#!/bin/sh
GALAXY_LIB="%s"
if [ "$GALAXY_LIB" != "None" ]; then
--- a/lib/galaxy/jobs/runners/sge.py Fri Feb 11 09:27:10 2011 -0500
+++ b/lib/galaxy/jobs/runners/sge.py Fri Feb 11 13:12:27 2011 -0500
@@ -8,27 +8,42 @@
import pkg_resources
+egg_message = """
+
+The 'sge' runner depends on 'DRMAA_python' which is not installed. Galaxy's
+"scramble" system should make this installation simple, please follow the
+instructions found at:
+
+ http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
+
+Additional errors may follow:
+%s
+"""
+
+
try:
pkg_resources.require( "DRMAA_python" )
- DRMAA = __import__( "DRMAA" )
-except:
- DRMAA = None
+ import DRMAA
+except Exception, e:
+ raise Exception( egg_message % str( e ) )
+
log = logging.getLogger( __name__ )
-if DRMAA is not None:
- DRMAA_state = {
- DRMAA.Session.UNDETERMINED: 'process status cannot be determined',
- DRMAA.Session.QUEUED_ACTIVE: 'job is queued and waiting to be scheduled',
- DRMAA.Session.SYSTEM_ON_HOLD: 'job is queued and in system hold',
- DRMAA.Session.USER_ON_HOLD: 'job is queued and in user hold',
- DRMAA.Session.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold',
- DRMAA.Session.RUNNING: 'job is running',
- DRMAA.Session.SYSTEM_SUSPENDED: 'job is system suspended',
- DRMAA.Session.USER_SUSPENDED: 'job is user suspended',
- DRMAA.Session.DONE: 'job finished normally',
- DRMAA.Session.FAILED: 'job finished, but failed',
- }
+__all__ = [ 'SGEJobRunner' ]
+
+DRMAA_state = {
+ DRMAA.Session.UNDETERMINED: 'process status cannot be determined',
+ DRMAA.Session.QUEUED_ACTIVE: 'job is queued and waiting to be scheduled',
+ DRMAA.Session.SYSTEM_ON_HOLD: 'job is queued and in system hold',
+ DRMAA.Session.USER_ON_HOLD: 'job is queued and in user hold',
+ DRMAA.Session.USER_SYSTEM_ON_HOLD: 'job is queued and in user and system hold',
+ DRMAA.Session.RUNNING: 'job is running',
+ DRMAA.Session.SYSTEM_SUSPENDED: 'job is system suspended',
+ DRMAA.Session.USER_SUSPENDED: 'job is user suspended',
+ DRMAA.Session.DONE: 'job finished normally',
+ DRMAA.Session.FAILED: 'job finished, but failed',
+}
sge_template = """#!/bin/sh
#$ -S /bin/sh
@@ -67,9 +82,6 @@
STOP_SIGNAL = object()
def __init__( self, app ):
"""Initialize this job runner and start the monitor thread"""
- # Check if SGE was importable, fail if not
- if DRMAA is None:
- raise Exception( "SGEJobRunner requires DRMAA_python which was not found" )
self.app = app
self.sa_session = app.model.context
# 'watched' and 'queue' are both used to keep track of jobs to watch.
--- a/lib/galaxy/jobs/runners/tasks.py Fri Feb 11 09:27:10 2011 -0500
+++ b/lib/galaxy/jobs/runners/tasks.py Fri Feb 11 13:12:27 2011 -0500
@@ -12,6 +12,8 @@
log = logging.getLogger( __name__ )
+__all__ = [ 'TaskedJobRunner' ]
+
class TaskedJobRunner( object ):
"""
Job runner backed by a finite pool of worker threads. FIFO scheduling
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/68c394e5dda8/
changeset: r5046:68c394e5dda8
user: guru
date: 2011-02-11 15:27:10
summary: Updated path to sputnik binary in 'Extract orthologous microsatellites for multiple (>2) species alignments' tool
affected #: 1 file (52 bytes)
--- a/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl Fri Feb 11 08:42:05 2011 -0500
+++ b/tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl Fri Feb 11 09:27:10 2011 -0500
@@ -18,7 +18,7 @@
#-------------------------------------------------------------------------------
# WHICH SPUTNIK USED?
my $sputnikpath = ();
-$sputnikpath = "/Users/ydk/work/rhesus_microsat/codes/./sputnik_Mac-PowerPC";
+$sputnikpath = "sputnik";
#print "sputnik_Mac-PowerPC non-existant\n" if !-e $sputnikpath;
#exit if !-e $sputnikpath;
#$sputnikpath = "bx-sputnik" ;
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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