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Getting "FATAL: sorry, too many clients already" in postgres database
by Anthonius deBoer 27 Jun '13

27 Jun '13

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 adjusted database_engine_option_pool_size = 20 database_engine_option_max_overflow = 40 already but maybe I set those too high? What is a normal setting for max_connections in galaxy production servers? Thanks, Thon

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Dataset appears as running job in history when changing datatype
by Julien SEILER 27 Jun '13

27 Jun '13

Dear all, We are running a local Galaxy instance up-to-date against galaxy/galaxy-dist. When we edit attributes of a dataset in current history and request a datatype change (Datatype tab), the selected dataset appears as a running job (yellow box with spinning icon) for ever. The type has been changed and if we refresh the history manually, the dataset appears in green again. Is anyone experiencing the same issue ? Regards, Julien -- Julien Seiler IGBMC Directeur des systèmes d'information Email : julien.seiler(a)igbmc.fr Tel : 03 88 65 33 63

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Any Galaxers working on GenomeSpace, going to Oslo?
by Samuel Lampa 27 Jun '13

27 Jun '13

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

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Extra authentication
by shashi shekhar 27 Jun '13

27 Jun '13

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

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Problem installing tools on cloud instance
by Brad Zeitner 27 Jun '13

27 Jun '13

I've started up an instance using cloudman, and it seemed to be running fine. When I tried to install a tool from the toolshed I got an error, and in trying to resolve the error I used the admin console to update galaxy. Now when Galaxy tries to start I get the following error: galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,969 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,970 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2013-06-26 22:20:49,970 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.tools.data DEBUG 2013-06-26 22:20:49,988 Loaded tool data table 'all_fasta' galaxy.tools.data DEBUG 2013-06-26 22:20:49,988 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2013-06-26 22:20:49,989 Loaded tool data table 'bowtie_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,989 Loaded tool data table 'bowtie_indexes_color' galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table 'lastz_seqs' galaxy.tools.data DEBUG 2013-06-26 22:20:49,990 Loaded tool data table 'perm_base_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,996 Loaded tool data table 'perm_color_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,996 Loaded tool data table 'sam_fa_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table 'picard_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table 'srma_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,997 Loaded tool data table 'tophat_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table 'mosaik_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table 'sam_indexes' galaxy.tools.data DEBUG 2013-06-26 22:20:49,998 Loaded tool data table 'twobit' galaxy.tools.data DEBUG 2013-06-26 22:20:49,999 Loaded tool data table 'lift_over' Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py", line 95, in __init__ from_shed_config=False ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", line 56, in load_from_config_file tree = util.parse_xml( config_filename ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/util/__init__.py", line 132, in parse_xml tree = ElementTree.parse(fname) File "/mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 576, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: './shed_tool_data_table_conf.xml' Removing PID file paster.pid How do I resolve the no such file or directory error? I found an email conversation on this that said to restart galaxy, and I've done this multiple times but the problem is persisting. Thanks, -Brad

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DRMAA Runner URL Specify TORQUE host
by Bart Gottschalk 26 Jun '13

26 Jun '13

Is it possible to specify the torque host as part of a DRMAA runner URL? I haven't been able to find a *native_options *parameter to allow for this. I'm using the old style cluster configuration. *drmaa://[native_options]/* * * Also, I haven't been able to find a list of native_options anywhere. Does anyone have a link to a comprehensive list? - Bart

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Styling the Galaxy tool config xml
by graham etherington (TSL) 26 Jun '13

26 Jun '13

Hi, I'm trying to see if I can style Galaxy tools, so instead of all the input fields being a long list one after the other, I can align a few of the fields side-by-side. Has anyone any suggestions on how I might accomplish this? Best wishes, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601

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Fwd: How to Clean up Old Data
by greg 26 Jun '13

26 Jun '13

(I'm resending this, it didn't seem to go through) ---------- Forwarded message ---------- From: greg <margeemail(a)gmail.com> Date: Thu, Jun 13, 2013 at 9:29 AM Subject: Re: [galaxy-dev] How to Clean up Old Data To: Björn Grüning <bjoern.gruening(a)pharmazie.uni-freiburg.de> Cc: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> Hi Bjorn, Could I have a look at your cron job for this? I'm not completely sure what to schedule. Thanks, Greg On Mon, Mar 11, 2013 at 1:17 PM, greg <margeemail(a)gmail.com> wrote: > Thanks. Could I have a look at what your cron job looks like? > > -Greg > > On Mon, Mar 11, 2013 at 11:58 AM, Björn Grüning > <bjoern.gruening(a)pharmazie.uni-freiburg.de> wrote: >> Hi Greg, >> >>> I'm trying to figure out how to reduce the data stored on the galaxy server. >>> >>> I came across this page and it looks like data will get deleted if the >>> history element gets deleted but I can't tell if this happens >>> automatically or if I need to cron these scripts: >>> http://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20… >>> >>> Is there anything else I can do to clean up unused data? >> >> No that should be sufficient. You need to run >> >> python cleanup_datasets.py universe_wsgi.ini -d 60 >> >> with the different parameters ... -1 -2 -3 .... >> It will not happen automatically, i recommend you to set up a cron job >> that runs every week. You also may want to change the -d 60 to something >> less than 60. >> >>> Also is there a way a user can keep her history around as a record of >>> what was done and be able to rerun it later, but still delete the >>> actual data? >> >> I don't think that is possible at the moment. >> Cheers, >> Bjoern >> >>> Thanks, >>> >>> Greg >>> ___________________________________________________________ >>> 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/ >> >>

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Bowtie2 Specifying -k value (Alignment Search)
by Adam Brenner 26 Jun '13

26 Jun '13

One of our users has requested to see if we could add specifying an alignment search option to Bowtie2 (-k and -a option http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#default-mode-search-… ) Is this something anyone else has added to their galaxy installs? If so, how? I was looking at galaxy/dist/tools/sr_mapping/bowtie2_wrapper.* and it does not seem to challenging to add another field where a user could specify some integer value that we simply pass to the the <command> tag in the xml file. Would this be the correct way to go about this? Thanks in advanced! -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/ aebrenne(a)uci.edu

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Re: [galaxy-dev] How to enable auto option for newly added file formats
by Peter Cock 26 Jun '13

26 Jun '13

On Tue, Jun 25, 2013 at 8:28 AM, shashi shekhar <me_shashi29(a)yahoo.co.in> wrote: > Hi, > > yeah ..it is same thing... but i followed the galaxy -datatype(how to add > new file format)tutorial ..but still my newly added file format is not > working with auto option ....it always display txt format ..it is similar to > txt format with some specific property .. > > Reagrds > shashi So you've followed this: http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes Have you tested your sniff method works? Have you checked the order the file types are tested? Peter P.S. Don't forget to CC the mailing list.

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