[galaxy-dev] galaxy install nginx
dear sir: nginx postgress galaxy which one first install ? ngsf...@hygenomics.com ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Torque Exec Exception
hi all: galaxy.jobs.runners.cli_job.torque WARNING 2014-03-07 11:23:33,764 No valid qstat XML return from `qstat -x`, got the following: galaxy.jobs.runners ERROR 2014-03-07 11:23:33,765 Unhandled exception checking active jobs Traceback (most recent call last): File /share/home/ldapuser/main/lib/galaxy/jobs/runners/__init__.py, line 339, in monitor self.check_watched_items() File /share/home/ldapuser/main/lib/galaxy/jobs/runners/cli.py, line 150, in check_watched_items job_states = self.__get_job_states() File /share/home/ldapuser/main/lib/galaxy/jobs/runners/cli.py, line 202, in __get_job_states job_states.update(job_interface.parse_status(cmd_out.stdout, job_ids)) TypeError: 'NoneType' object is not iterable #qmgr -c p q batch create queue batch set queue batch queue_type = Execution set queue batch enabled = True set queue batch started = True Finish the torque tasks ， throw exceptions in the log file。 ngsf...@hygenomics.com___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Torque.py Bug
Hi,
base:
os:centos6.4
torque:4.2.7
I built a glaxy cluster today,and then I found the job completion status of
torque queue is 'c',but the need state of galalxy is ok.So I modified the
torque.py file and solved this error. I do, right?
diff -r 8411a9f30feb lib/galaxy/jobs/runners/cli_job/torque.py
--- a/lib/galaxy/jobs/runners/cli_job/torque.py Thu Dec 19 14:38:03 2013 -0500
+++ b/lib/galaxy/jobs/runners/cli_job/torque.py Fri Feb 28 13:02:48 2014 +0800
@@ -117,6 +117,8 @@
if id in job_ids:
state = job.find('job_state').text
# map PBS job states to Galaxy job states.
+if state == u'C' :
+state = 'ok'
rval[id] = self.__get_job_state(state)
return rval
ngsf...@hygenomics.com___
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[galaxy-dev] tool of installing tool shed repositories
Hi, there: I'm currently trying to migrate all repositories of main tool shed on http://toolshed.g2.bx.psu.edu/ to local, but got some problems. I'm wondering whether there is an existing tool can automatically do the job? thanks rgds, Ray ngsf...@hygenomics.com[5UQ[BL(6~BS2JV6(11-04-16-34-29).png___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Fw: Re: tool of installing tool shed repositories
ngsf...@hygenomics.com From: ngsf...@hygenomics.com Date: 2013-11-04 17:53 To: Björn Grüning Subject: Re: Re: [galaxy-dev] tool of installing tool shed repositories hi Bjoern: I am trying to bulk import repositories, by developing some tools following the thought similar to those in toolshed tools test. I just want to make sure whether there are some tools already exist. rgds, Ray ngsf...@hygenomics.com From: Björn Grüning Date: 2013-11-04 16:46 To: ngsf...@hygenomics.com CC: galaxy-dev Subject: Re: [galaxy-dev] tool of installing tool shed repositories Hi Ray, there is some work in that direction to easily import and export repositories. The export feature is already integrated and should help you. You will end up with a tarball with all informations about that repository and the import should be easier. If you want to work on the import part, I think your work is more than welcome! Cheers, Bjoern Hi, there: I'm currently trying to migrate all repositories of main tool shed on http://toolshed.g2.bx.psu.edu/ to local, but got some problems. I'm wondering whether there is an existing tool can automatically do the job? thanks rgds, Ray __ ngsf...@hygenomics.com ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] tool of installing tool shed repositories
Hi, there: I'm currently trying to migrate all repositories of main tool shed on http://toolshed.g2.bx.psu.edu/ to local, but got some problems. I'm wondering whether there is an existing tool can automatically do the job? thanks rgds, Ray ngsf...@hygenomics.com[5UQ[BL(6~BS2JV6W}N6[%S.png___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
