[galaxy-dev] Extra authentication
Hi, i have installed local instance of galaxy in my linux system. i want to add an extra authentication mechanism before saving user information into database in which file i have to do modification .? regards shashi ___ 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] Any Galaxers working on GenomeSpace, going to Oslo?
Hi, At UPPMAX, are interested both in Galaxy, and the GenomeSpace project[1], and wanted to check if there are people on the Galaxy team or other galaxers who are involved in the GenomeSpace project, that will be in Oslo next week? If so, I would be interested to meet up! BestRegards // Samuel -- Developer at SNIC-UPPMAX www.uppmax.uu.se Developer at Dept of Pharm Biosciences www.farmbio.uu.se ___ 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 Dependency Check for eXpress - requirements syntax incorrect?
Howdy, One of our users is running the eXpress package under NGS: RNA Analysis - eXpress -- galaxy/dist/tools/ngs_rna/express_wrapper.* I noticed the syntax for express_wrapper.xml has the following: requirement type=binaryeXpress/requirement any reason why it was set to that, as opposed to: requirement type=packageeXpress/requirement In our setup, we need to source the env.sh file for express to setup the correct environmental variables. Changing from binary to package has not solved this and re-running the job never sources our env.sh file. What am I doing wrong? My tool dependency directory looks like so: galaxy/dist/tool_dependency/eXpress/ |---default -- 1.3.0 |1.3.0/env.sh Thanks, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.edu ___ 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] Getting FATAL: sorry, too many clients already in postgres database
Hi,I am getting the error "FATAL: sorry, too many clients already" in in my local Galaxy instance in the POSTGRES database log.I have set max_connections = 1000 in already in "postgresql.conf" and STILL get this error...I was running a Flowcell with about 96 samples and a workflow with about 50 steps each, but I never had a problem before when max_connections was set to 100 and did not change the database...I do have a cluster that is much faster so i guess there may be several connections going to the database, but maybe there is some leakage in the galaxy code that is not closing the connections?It really screws up the galaxy instance and jobs are just in limbo and never finsihed (in the database)...Any ideas?I adjusteddatabase_engine_option_pool_size = 20database_engine_option_max_overflow = 40already but maybe I set those too high?What is a normal setting for max_connections in galaxy production servers?Thanks,Thon___ 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/
Re: [galaxy-dev] Tool Dependency Check for eXpress - requirements syntax incorrect?
James, Thanks for the response. I had some sort of typo in my express_wrapper.xml file and all is well now. It is now sourcing the correct file. I went ahead and submitted a pull request to have eXpress updated to package, instead of binary: https://bitbucket.org/galaxy/galaxy-central/pull-request/192/express-tool-requirements-tag-updated/diff -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.edu On Thu, Jun 27, 2013 at 11:03 AM, James Taylor ja...@jamestaylor.org wrote: Hi Adam, yes, it should be package, the binary type has never been supported but keeps getting propagated for some reason. At some point it might be nice to have a configurable mapping from the other dependency types to packages. However, changing it to package *should* work. Can you send the relevant part of the paster log, it should log information about dependency resolution and the command line. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Thu, Jun 27, 2013 at 1:38 PM, Adam Brenner aebre...@uci.edu wrote: Howdy, One of our users is running the eXpress package under NGS: RNA Analysis - eXpress -- galaxy/dist/tools/ngs_rna/express_wrapper.* I noticed the syntax for express_wrapper.xml has the following: requirement type=binaryeXpress/requirement any reason why it was set to that, as opposed to: requirement type=packageeXpress/requirement In our setup, we need to source the env.sh file for express to setup the correct environmental variables. Changing from binary to package has not solved this and re-running the job never sources our env.sh file. What am I doing wrong? My tool dependency directory looks like so: galaxy/dist/tool_dependency/eXpress/ |---default -- 1.3.0 |1.3.0/env.sh Thanks, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.edu ___ 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] history item status not updating
I submitted a workflow that in turn submits a drm job to sun grid engine. The queue had an error (probably due to a problem with automount). Traceback (most recent call last): File /inside/depot4/galaxy/lib/galaxy/jobs/runners/__init__.py, line 60, in run_next method(arg) File /inside/depot4/galaxy/lib/galaxy/jobs/runners/drmaa.py, line 169, in queue_job external_job_id = self.ds.runJob(jt) File /inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/__init__.py, line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File /inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/helpers.py, line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer File /inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/errors.py, line 90, in error_check raise _ERRORS[code-1](code %s: %s % (code, error_buffer.value)) DeniedByDrmException: code 17: error: no suitable queues When the sysadmin cleared the error, the job started running normally after being in an error state for 10 minutes. The cool thing is that galaxy kept running without a problem. galaxy.jobs.runners.drmaa DEBUG 2013-06-27 14:51:22,968 (10481/4767487) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2013-06-27 15:00:23,628 (10481/4767487) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2013-06-27 15:00:27,751 (10481/4767487) state change: job is running However in the history panel, the job shows as queued but not running, even if I refresh the history panel. Is this normal or should the status change to running? I'm using this version of straight galaxy: changeset: 10162:f295092476c7 branch: stable parent: 10160:2efb1083676b user:Dannon Baker dannonba...@me.com date:Sat Jun 15 09:08:09 2013 -0400 summary: Fix reports import issue reported by Lance, https://trello.com/card/bug-in-reports-webapp-imports/506338ce32ae458f6d15e4b3/943 -Robert Baertsch UC Santa Cruz ___ 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] Managing a sequencer
Hi, I am wondering how the nglims Manage sequencers and external services works. I want to add our MiSeq such that all future runs show up in Galaxy as data sets. Is this the way to do it? When I use this menu to add our sequencer it asks for a username, ip address, password, etc. I am not sure what it is really asking for actually. All of the data from the MiSeq shows up on the same computer as Galaxy, and so I am sure that I do not need an IP address except for localhost. Is there any beginning documentation on this part of nglims? Or a tutorial on how to detect new data and import it? Thanks. -- Lee Katz, Ph.D. ___ 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/
Re: [galaxy-dev] history item status not updating
ignore this last post On Jun 27, 2013, at 3:09 PM, Robert Baertsch wrote: I submitted a workflow that in turn submits a drm job to sun grid engine. The queue had an error (probably due to a problem with automount). Traceback (most recent call last): File /inside/depot4/galaxy/lib/galaxy/jobs/runners/__init__.py, line 60, in run_next method(arg) File /inside/depot4/galaxy/lib/galaxy/jobs/runners/drmaa.py, line 169, in queue_job external_job_id = self.ds.runJob(jt) File /inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/__init__.py, line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File /inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/helpers.py, line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer File /inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/errors.py, line 90, in error_check raise _ERRORS[code-1](code %s: %s % (code, error_buffer.value)) DeniedByDrmException: code 17: error: no suitable queues When the sysadmin cleared the error, the job started running normally after being in an error state for 10 minutes. The cool thing is that galaxy kept running without a problem. galaxy.jobs.runners.drmaa DEBUG 2013-06-27 14:51:22,968 (10481/4767487) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2013-06-27 15:00:23,628 (10481/4767487) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2013-06-27 15:00:27,751 (10481/4767487) state change: job is running However in the history panel, the job shows as queued but not running, even if I refresh the history panel. Is this normal or should the status change to running? I'm using this version of straight galaxy: changeset: 10162:f295092476c7 branch: stable parent: 10160:2efb1083676b user:Dannon Baker dannonba...@me.com date:Sat Jun 15 09:08:09 2013 -0400 summary: Fix reports import issue reported by Lance, https://trello.com/card/bug-in-reports-webapp-imports/506338ce32ae458f6d15e4b3/943 -Robert Baertsch UC Santa Cruz ___ 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/
