August 2012 - galaxy-dev - lists.galaxyproject.org

Emailing to all our Galaxy users
by Joachim Jacob 06 Aug '12

06 Aug '12

Dear devs, How can I extract a list of the email addresses of all users of our Galaxy? Cheers, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Re: [galaxy-dev] Error in loading tools.
by Nikhil Joshi 04 Aug '12

04 Aug '12

On Fri, Aug 3, 2012 at 11:07 PM, Nikhil Joshi <najoshi(a)ucdavis.edu> wrote: > Hey Mo, > > So I'm figuring out the same issues, and I think I have been able to > figure it out.... but for sure you need to uncomment the > tool_config_file and tool_path lines in your universe_wsgi.ini file, > probably should create a new directory one above your install > directory called "shed_tools", and then restart galaxy. I also ran > into the problem where I needed to create a TMPDIR shell variable that > pointed to the correct tmp directory. I know you guys don't like the > command line, so if this sounds like gibberish to you, I'm hoping the > galaxy team can provide a simpler solution. > > - Nik. > > P.S. I'm working on creating a DESeq repository that can be > automatically installed from the toolbox. I will let you know when I > am successful. It was nice to meet you at the conference! :) > > On Wed, Aug 1, 2012 at 9:07 AM, Mohammad Heydarian <mheydarian(a)gmail.com> wrote: >> Thanks for this. >> >> I updated my local version of Galaxy Cloudman and tried loading a tool and >> got a new error: >> >> The tool_config_file setting in universe_wsgi.ini must include at least one >> shed tool configuration file name with a <toolbox> tag that includes a >> tool_path attribute value which is a directory relative to the Galaxy >> installation directory in order to automatically install tools from a Galaxy >> tool shed (e.g., the file name shed_tool_conf.xml whose <toolbox> tag is >> <toolbox tool_path="../shed_tools">). >> >> See the Automatic installation of Galaxy tool shed repository tools into a >> local Galaxy instance section of the Galaxy tool shed wiki for all of the >> details. >> >> >> Any help interpreting this would be greatly appreciated! >> >> >> >> Cheers, >> >> Mo Heydarian >> >> >> >> >> On Tue, Jul 31, 2012 at 4:11 PM, Dannon Baker <dannonbaker(a)me.com> wrote: >>> >>> The problem here is that the public toolshed interface has been updated >>> more recently than the galaxy install on that cloud instance. You should >>> be good to go if you update galaxy (possible through the admin interface at >>> <your_ec2_instance>/cloud/admin/) to the latest version. >>> >>> -Dannon >>> >>> On Jul 31, 2012, at 12:11 PM, Mohammad Heydarian <mheydarian(a)gmail.com> >>> wrote: >>> >>> > Hi Galaxy Community! >>> > Hope all is well. >>> > >>> > I've been trying to install some tools in my Galaxy Cloudman instance >>> > (using image: ami-da58aab3 ) from the main toolshed. When I try to "install >>> > to local Galaxy" I get the error: >>> > >>> > Not Found >>> > >>> > The resource could not be found. >>> > No action for /admin_toolshed/prepare_for_install >>> > >>> > >>> > >>> > I have tried to load tools on a couple of different Cloudman instances >>> > and tried to load a variety of tools and end up with the same error. Any >>> > help would be fantastic. >>> > >>> > Cheers, >>> > Mo Heydarian >>> > >>> > >>> > >>> > ___________________________________________________________ >>> > 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/ >>> >> >> >> ___________________________________________________________ >> 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/ > > > > -- > Nikhil Joshi > Bioinformatics Analyst/Programmer > UC Davis Bioinformatics Core > http://bioinformatics.ucdavis.edu/ > najoshi -at- ucdavis -dot- edu > 530.752.2698 (w) -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)

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Toolshed: disabling registering
by Joachim Jacob 03 Aug '12

03 Aug '12

Hi, Can I disable the account creation by users in our Galaxy tool shed? Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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genbank data type
by Marc Logghe 03 Aug '12

03 Aug '12

Hi all, The last few days I have been experimenting with a local Galaxy installation. Via the tool shed, emboss and emboss_datatypes were installed. Next, a custom tool was added for which a rich sequence is needed as input. I was hoping to achieve this as such: <param name="input" type="data" format="genbank" label="Annotated sequences"/> As a test, a genbank was created using EMBOSS's newseq and output format genbank was chosen (the history indicates the format is 'genbank', so that's fine). However, it seems not to be recognized as valid input for our custom tool. Guess I'm overlooking something obvious ? Regards, Marc ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx(a)ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________

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Strange "Could not moveŠ." error
by Iry Witham 02 Aug '12

02 Aug '12

Hi Dev-Team, I am experiencing a strange error that I cannot replicate on two identical instances of my Galaxy server. I have a tool that runs fine on my test instance and fails on my development instance. The servers are identically configured and running the same build. The handler.log from the successful instance shows the following: galaxy.jobs DEBUG 2012-08-02 11:31:07,881 (295) Working directory for job is: /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295 galaxy.jobs.handler DEBUG 2012-08-02 11:31:07,881 dispatching job 295 to pbs runner galaxy.jobs.handler INFO 2012-08-02 11:31:08,083 (295) Job dispatched galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) submitting file /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/pbs/295.sh galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) command is: perl /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/tools/jax_cnv/cnv-seq.pl --out-basename cnv_seq_result --test /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1504.dat --ref /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1503.dat --genome-size 2716965481 --p-value 0.001 --bigger-window 1.5 --no-annotate --log2-threshold 0.6; cd /hpcdata/galaxy-test/galaxy-setup/galaxy-dist; /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/set_metadata.sh ./database/files /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295 . /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/universe_wsgi.ini /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/tmp/tmplTSKeF /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/galaxy.json /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_in_HistoryDatasetAssociation_689_Oh21hx,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_kwds_HistoryDatasetAssociation_689_xgxlZy,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_out_HistoryDatasetAssociation_689_H0claK,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_results_HistoryDatasetAssociation_689_rdQBs8,,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_override_HistoryDatasetAssociation_689_B0U0MV galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,395 (295) queued in default queue as 112605.scyld.localdomain galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,776 (295/112605.scyld.localdomain) PBS job state changed from N to R galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,117 (295/112605.scyld.localdomain) PBS job state changed from R to C galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,118 (295/112605.scyld.localdomain) PBS job has completed successfully galaxy.jobs DEBUG 2012-08-02 11:31:27,197 finish(): Moved /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/cnv_seq_result.cnv to /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1555.dat as directed by from_work_dir galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,249 loading metadata from file for: HistoryDatasetAssociation 689 galaxy.jobs DEBUG 2012-08-02 11:31:27,382 job 295 ended galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,382 Cleaning up external metadata files The same log from the failing instance shows the following: galaxy.jobs DEBUG 2012-08-02 11:54:29,234 (113) Working directory for job is: /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113 galaxy.jobs.handler DEBUG 2012-08-02 11:54:29,234 dispatching job 113 to pbs runner galaxy.jobs.handler INFO 2012-08-02 11:54:29,420 (113) Job dispatched galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,669 (113) submitting file /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/pbs/113.sh galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,669 (113) command is: perl /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/tools/jax_cnv/cnv-seq.pl --out-basename cnv_seq_result --test /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/files/000/dataset_131.dat --ref /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/files/000/dataset_132.dat --genome-size 2716965481 --p-value 0.001 --bigger-window 1.5 --no-annotate --log2-threshold 0.6; cd /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist; /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/set_metadata.sh ./database/files /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113 . /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/universe_wsgi.ini /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/tmp/tmpgTn7ey /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/galaxy.json /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_in_HistoryDatasetAssociation_136_VYG968,/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_kwds_HistoryDatasetAssociation_136_yo_4aK,/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_out_HistoryDatasetAssociation_136_D6HwmI,/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_results_HistoryDatasetAssociation_136_zunslF,,/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_override_HistoryDatasetAssociation_136_FDUxso galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,680 (113) queued in default queue as 112609.scyld.localdomain galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:30,163 (113/112609.scyld.localdomain) PBS job state changed from N to R galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:33,298 (113/112609.scyld.localdomain) PBS job state changed from R to C galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:33,298 (113/112609.scyld.localdomain) PBS job has completed successfully galaxy.jobs DEBUG 2012-08-02 11:54:33,354 finish(): Could not move /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/cnv_seq_result.cnv to /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/files/000/dataset_140.dat as directed by from_work_dir galaxy.jobs DEBUG 2012-08-02 11:54:33,467 job 113 ended Why would one fail and the other succeed? Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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Re: [galaxy-dev] [galaxy-user] Fwd: Local instance and storage space to provide
by Scott McManus 01 Aug '12

01 Aug '12

Sorry - I fouled up and should have kept this on galaxy-dev. -Scott ----- Original Message ----- > > I'm forwarding this to galaxy-user instead of galaxy-dev. > > -Scott > > ----- Forwarded Message ----- > From: "Scott McManus" <scottmcmanus(a)gatech.edu> > To: "Sarah Maman" <sarah.maman(a)toulouse.inra.fr> > Cc: galaxy-dev(a)lists.bx.psu.edu > Sent: Wednesday, August 1, 2012 4:18:29 PM > Subject: Re: [galaxy-dev] Local instance and storage space to provide > > > Hi Sarah- > > I'm sure others have experiences that could help, so I hope they will > chime in. Nate put together some slides two years ago on production > setups, > including some architecture for the server main.g2.bx.psu.edu: > http://wiki.g2.bx.psu.edu/Events/GDC2010?action=AttachFile&do=get&target=GD… > > There is also a wiki page describing production environments: > http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server > > Again, I'm sure others have had different experiences with both more > and less > hardware on hand. Of course your mileage may vary based on the tools > being used > (which in your case I'm guessing is Tophat), the number of datasets > that will > need to be analyzed, and so on. > > I hope that helps! > > -Scott > > ----- Original Message ----- > > Dear all, > > > > To purchase equipment related to a local instance of Galaxy, I > > would > > like to have your feedback. > > > > Did you notice load problems when 10 to 20 users launch jobs at the > > same > > time and on a single instance of Galaxy, with mi-RNA or RNA seq > > data > > ? > > > > What do you recommend in terms of storage space, number of nodes, > > number > > of instances? > > > > Thank you in advance, > > Sarah Maman > > ___________________________________________________________ > > 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/ > > > ___________________________________________________________ > 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/ > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ >

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PBS Server Throwing Errors
by Daniel Patrick Sullivan 01 Aug '12

01 Aug '12

Hi, Galaxy Community, Greetings from The University of Chicago; I hope all who attended the Galaxy conference enjoyed it as much as I did. I have searched the mailing list archives as well as Google to a resolve problem I am seeing, however I am somewhat at a loss as to the next course of action I should be taking to bring this issue to a close. I am hoping that one of the bright minds on this mailing list could help me shed some light on the solution to my problem, or at least help me identify a root cause. I have configured Galaxy to integrate with TORQUE (version 4.0.2) server, and successfully built the PBS python egg as specified in the Galaxy documentation. I am using Python version 2.6 and the latest build of Galaxy. Whenever I launch a job from the Galaxy UI, I get the following error message(s) on the PBS server: 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting version numbers, 1 detected, 2 expected 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply code=15058(Bad DIS based Request Protocol MSG=cannot decode message), aux=0, type=AlternateUserAuthentication, from galaxy@ 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting version numbers, 1 detected, 2 expected 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply code=15058(Bad DIS based Request Protocol MSG=cannot decode message), aux=0, type=QueueJob, from galaxy@ 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting version numbers, 1 detected, 2 expected 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply code=15058(Bad DIS based Request Protocol MSG=cannot decode message), aux=0, type=Disconnect, from galaxy@ 07/30/2012 15:43:01;0002;PBS_Server;Svr;PBS_Server;Torque Server Version = 4.0.2, loglevel = 1 One thing I did notice, that suggests there might be a problem, is that there is no hostname after the galaxy@; most of the other messages in this log file have a host name appended to log entry, i.e.: 07/30/2012 15:43:38;0100;PBS_Server;Req;;Type StatusJob request received from root@sc01, sock=10 I have completed a tcpdump on the schedule node, and I can definitely see bi-directional traffic between the Galaxy server and the scheduler node on TCP port 15001. In addition to this, I have installed the TORQUE client tools on on the Galaxy server, and can spawn an interactive job with qsub -I, as well as check the status of queued jobs using qstat (from the Galaxy server). This suggests to me that there a potential problem with the PBS Egg, although I am not certain. Has anybody seen something like this before, or could somebody point me in the right direction? We do have a support contract with Adaptive Computing, and I am opening a ticket with them as well, however I wanted to reach out to the Galaxy community to cover all of my bases. Thank-you so much for taking the time to read my email. Dan Sullivan

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Local instance and storage space to provide
by Sarah Maman 01 Aug '12

01 Aug '12

Dear all, To purchase equipment related to a local instance of Galaxy, I would like to have your feedback. Did you notice load problems when 10 to 20 users launch jobs at the same time and on a single instance of Galaxy, with mi-RNA or RNA seq data ? What do you recommend in terms of storage space, number of nodes, number of instances? Thank you in advance, Sarah Maman

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Update Galaxy instance with Mercurial error
by Makis Ladoukakis 01 Aug '12

01 Aug '12

Dear Galaxy users, I am running a Galaxy instance in my institution's server and I want to keep it up to date with the latest release. Nevertheless when i try hg incoming i get the following error: abort: There is no Mercurial repository here (.hg not found)! Most probably the administrator of the server has downloaded the Galaxy-dist directory without the use of Mercurial (I was suspicious of that all along as the directory of the Galaxy installation is named galaxy_dist and not galaxy-dist). Is there another way to update my instance? Thank you, Makis Ladoukakis

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Error in loading tools.
by Mohammad Heydarian 01 Aug '12

01 Aug '12

Hi Galaxy Community! Hope all is well. I've been trying to install some tools in my Galaxy Cloudman instance (using image: ami-da58aab3 ) from the main toolshed. When I try to "install to local Galaxy" I get the error: Not Found The resource could not be found. No action for /admin_toolshed/prepare_for_install I have tried to load tools on a couple of different Cloudman instances and tried to load a variety of tools and end up with the same error. Any help would be fantastic. Cheers, Mo Heydarian

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