3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1f1072317efd/ changeset: 1f1072317efd branch: stable user: natefoo date: 2013-02-12 14:46:28 summary: Allow the CLI runner to handle command stdout >65K. affected #: 2 files diff -r 961ae35ba61230ac1f5991b7629e5da0559cd0b5 -r 1f1072317efd5cf82cb791d75ba968c4bacffaf4 lib/galaxy/jobs/runners/cli.py --- a/lib/galaxy/jobs/runners/cli.py +++ b/lib/galaxy/jobs/runners/cli.py @@ -316,6 +316,7 @@ if which_try == self.app.config.retry_job_output_collection: stdout = '' stderr = 'Job output not returned from cluster' + exit_code = 0 log.debug( stderr ) else: time.sleep(1) diff -r 961ae35ba61230ac1f5991b7629e5da0559cd0b5 -r 1f1072317efd5cf82cb791d75ba968c4bacffaf4 lib/galaxy/jobs/runners/cli_shell/rsh.py --- a/lib/galaxy/jobs/runners/cli_shell/rsh.py +++ b/lib/galaxy/jobs/runners/cli_shell/rsh.py @@ -4,6 +4,7 @@ import time import logging +import tempfile import subprocess from galaxy.util.bunch import Bunch @@ -28,7 +29,9 @@ fullcmd = '%s %s %s' % (self.rsh, self.hostname, cmd) else: fullcmd = '%s -l %s %s %s' % (self.rsh, self.username, self.hostname, cmd) - p = subprocess.Popen(fullcmd, shell=True, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + # Read stdout to a tempfile in case it's large (>65K) + outf = tempfile.TemporaryFile() + p = subprocess.Popen(fullcmd, shell=True, stdin=None, stdout=outf, stderr=subprocess.PIPE) # poll until timeout for i in range(timeout/3): r = p.poll() @@ -44,7 +47,8 @@ except: log.warning('Killing pid %s (cmd: "%s") with signal %s failed' % (p.pid, fullcmd, sig)) return Bunch(stdout='', stderr='Execution timed out', returncode=-1) - return Bunch(stdout=p.stdout.read(), stderr=p.stderr.read(), returncode=p.returncode) + outf.seek(0) + return Bunch(stdout=outf.read(), stderr=p.stderr.read(), returncode=p.returncode) class SecureShell(RemoteShell): https://bitbucket.org/galaxy/galaxy-central/commits/056ff69b05c4/ changeset: 056ff69b05c4 user: natefoo date: 2013-02-12 14:46:28 summary: Allow the CLI runner to handle command stdout >65K. affected #: 2 files diff -r e5dcefc328bb4fadcd0097787d167c7f43db5627 -r 056ff69b05c435f26650c5e7f65cffd764a40a08 lib/galaxy/jobs/runners/cli.py --- a/lib/galaxy/jobs/runners/cli.py +++ b/lib/galaxy/jobs/runners/cli.py @@ -316,6 +316,7 @@ if which_try == self.app.config.retry_job_output_collection: stdout = '' stderr = 'Job output not returned from cluster' + exit_code = 0 log.debug( stderr ) else: time.sleep(1) diff -r e5dcefc328bb4fadcd0097787d167c7f43db5627 -r 056ff69b05c435f26650c5e7f65cffd764a40a08 lib/galaxy/jobs/runners/cli_shell/rsh.py --- a/lib/galaxy/jobs/runners/cli_shell/rsh.py +++ b/lib/galaxy/jobs/runners/cli_shell/rsh.py @@ -4,6 +4,7 @@ import time import logging +import tempfile import subprocess from galaxy.util.bunch import Bunch @@ -28,7 +29,9 @@ fullcmd = '%s %s %s' % (self.rsh, self.hostname, cmd) else: fullcmd = '%s -l %s %s %s' % (self.rsh, self.username, self.hostname, cmd) - p = subprocess.Popen(fullcmd, shell=True, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + # Read stdout to a tempfile in case it's large (>65K) + outf = tempfile.TemporaryFile() + p = subprocess.Popen(fullcmd, shell=True, stdin=None, stdout=outf, stderr=subprocess.PIPE) # poll until timeout for i in range(timeout/3): r = p.poll() @@ -44,7 +47,8 @@ except: log.warning('Killing pid %s (cmd: "%s") with signal %s failed' % (p.pid, fullcmd, sig)) return Bunch(stdout='', stderr='Execution timed out', returncode=-1) - return Bunch(stdout=p.stdout.read(), stderr=p.stderr.read(), returncode=p.returncode) + outf.seek(0) + return Bunch(stdout=outf.read(), stderr=p.stderr.read(), returncode=p.returncode) class SecureShell(RemoteShell): https://bitbucket.org/galaxy/galaxy-central/commits/a6fe104c109f/ changeset: a6fe104c109f user: natefoo date: 2013-02-12 15:04:17 summary: Merged heads. affected #: 2 files diff -r 056ff69b05c435f26650c5e7f65cffd764a40a08 -r a6fe104c109feea61995567336a1aaf515acf0d5 tools/ngs_rna/tophat2_wrapper.py --- a/tools/ngs_rna/tophat2_wrapper.py +++ b/tools/ngs_rna/tophat2_wrapper.py @@ -22,7 +22,7 @@ parser.add_option( '', '--mate-std-dev', dest='mate_std_dev', help='Standard deviation of distribution on inner distances between male pairs.' ) parser.add_option( '', '--read-mismatches', dest='read_mismatches' ) parser.add_option( '', '--bowtie-n', action="store_true", dest='bowtie_n' ) - parser.add_option( '', '--report-discordant-pair-alignments', action="store_true", dest='report_discordant_pairs' ) + parser.add_option( '', '--no-discordant', action="store_true", dest='report_concordant_pairs_only' ) parser.add_option( '-a', '--min-anchor-length', dest='min_anchor_length', help='The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction.' ) parser.add_option( '-m', '--splice-mismatches', dest='splice_mismatches', help='The maximum number of mismatches that can appear in the anchor region of a spliced alignment.' ) @@ -141,8 +141,8 @@ opts = '-p %s %s' % ( options.num_threads, space ) if options.single_paired == 'paired': opts += ' -r %s' % options.mate_inner_dist - if options.report_discordant_pairs: - opts += ' --report-discordant-pair-alignments' + if options.report_concordant_pairs_only: + opts += ' --no-discordant' # Read group options. if options.rgid: if not options.rglb or not options.rgpl or not options.rgsm: diff -r 056ff69b05c435f26650c5e7f65cffd764a40a08 -r a6fe104c109feea61995567336a1aaf515acf0d5 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -37,8 +37,8 @@ -r $singlePaired.mate_inner_distance --mate-std-dev=$singlePaired.mate_std_dev - #if str($singlePaired.report_discordant_pairs) == "Yes": - --report-discordant-pair-alignments + #if str($singlePaired.report_discordant_pairs) == "No": + --no-discordant #end if #end if @@ -138,8 +138,8 @@ <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/><!-- Discordant pairs. --><param name="report_discordant_pairs" type="select" label="Report discordant pair alignments?"> - <option selected="true" value="No">No</option> - <option value="Yes">Yes</option> + <option value="No">No</option> + <option selected="True" value="Yes">Yes</option></param></when></conditional> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.