- galaxy-dev - lists.galaxyproject.org

Xenopus genome
by Kurtenbach, Stefan 09 Jun '16

09 Jun '16

Dear Galaxy team, First, thanks for your great work! I want to use Bowtie2 to align ChIPseq data to the Xenopus laevis genome. However, It's not listed. The tool said that if the desired genome is not in the list to contact the galaxy team, so here I am :) Could you add this? Thanks! Stefan

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Re: [galaxy-dev] How to get the encoded ID from the HistoryDatasetAssociation?
by Malcolm Tobias 08 Jun '16

08 Jun '16

Thanks Martin! With your hint and the example from graphviz.mako I was able to get this to work. Cheers, Malcolm On Wednesday, June 08, 2016 03:23:31 PM Martin Čech wrote: Hello Malcolm, encoded_id is a database row id that has been ran through this method (https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/security/__…) using the 'secret' from galaxy.ini config. You should be able to do something like this in the mako: ${trans.security.encode_id( hda.id[2] )} thank you for using Galaxy Martin On Wed, Jun 8, 2016 at 11:16 AM Malcolm Tobias <mtobias(a)wustl.edu[3]> wrote: hda.name[4] and hda.id[2] I can see various properties of thedataset, but not the encoded ID. Any suggestions on how to do this? Thanks in advance. Malcolm --Malcolm Tobias314.362.1594 ___________________________________________________________Please keep all replies on the list by using "reply all"in your mail client. To manage your subscriptions to thisand other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/[5] http://galaxyproject.org/search/mailinglists/[6] -- Malcolm Tobias 314.362.1594 -------- [1] https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/security/__… [2] http://hda.id [3] mailto:mtobias@wustl.edu [4] http://hda.name [5] https://lists.galaxyproject.org/ [6] http://galaxyproject.org/search/mailinglists/

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Any way to prime the value of a tool text field parameter dynamically?
by Dooley, Damion 08 Jun '16

08 Jun '16

I have a need to have the default value of a text parameter : <param name="statements" label="Statements" type="text" area="true" value="???"> Set dynamically, as powered by say a call to a function in <code file="tool_form.py" /> , much like a dynamic_options="get_rule_section(recipe_file)" call. Has anyone done that somehow without hacking Galaxy code? A user can then edit the text. The default depends on a previous selection (e.g. recipe_file input). Thanks, Damion

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not sure what I can do about this...
by Fernandez Edgar 08 Jun '16

08 Jun '16

Hello Gents, So someone asked me to install the package Prokka on Galaxy. I did and everything went well! However, the following error comes up, when they try to work with Prokka: Fatal error: Exit code 2 () [tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version. [20:20:53] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.10 from http://www.vicbioinformatics.com' -Z outdir\/prokka\.err -i outdir\/prokka\.fsa 2> /dev/null According to a google search, there is very little on this error. And it has been around for a while but I didn't find a posted solution. Any suggestions? Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218

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How to replace 'BioMart Central server' in the "Get Data" tools ?
by Hans-Rudolf Hotz 08 Jun '16

08 Jun '16

Hi As you probably know, the central BioMart server is currently unavailable (see: http://www.biomart.org/notice.html) Hence, the "Get Data -> BioMart Central server" tool in our local Galaxy installation does not work anymore - well, this is also the case on usegalaxy.org. We can easily switch the tool to point to a different Mart server, i.e.: Change: <inputs action="http://www.biomart.org/biomart/martview" .... to: <inputs action="http://www.ebi.ac.uk/uniprot/biomart/martview" .... However, we would like to switch to the ensembl Mart server: http://www.ensembl.org/biomart/martview It looks like the ensembl Mart server is nowadays embedded in the ensembl web site, and the requests are not send to Galaxy, but end up on the ensembl web page, where they cause a "Error 404 - Page not found". Unfortunately, I am not that savvy about the inner works of the ensembl web site anymore ;) Has anyone else looked into this problem and found already a solution? Thank you very much for any help Hans-Rudolf

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How to get the encoded ID from the HistoryDatasetAssociation?
by Malcolm Tobias 08 Jun '16

08 Jun '16

I'm really close to having a way to visualize radiological images in Galaxy, but need help in getting past the final hurdle. In the mako file, I can see how to pass parameters to the javascript that does the visualization. It's expecting a URL to the dataset, like: params["images"] = ["/datasets/78176dfc865c8302/display/"]; >From what I can gather 78176dfc865c8302 is the encoded ID for the dataset. >From variables like hda.name and hda.id I can see various properties of the dataset, but not the encoded ID. Any suggestions on how to do this? Thanks in advance. Malcolm -- Malcolm Tobias 314.362.1594

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Deploying custom genome in Galaxy for use with ANNOVAR
by David Kovalic 08 Jun '16

08 Jun '16

All, >From my read of the command line docs for ANNOVAR I believe that the program needs so ancillary files for its operation (e.g. GenePred file, transcripts fasta file, etc...). Does anyone have any experience deploying custom genomes in Galaxy for use with ANNOVAR? Specifically what files need to go where in order to enable the Galaxy ANNOVAR front end? Thanks, David

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Error installing cummeRbund tool
by Raymond Wan 07 Jun '16

07 Jun '16

Dear all, I'm trying to install a Galaxy tool (cummeRbund; the one from devteam) and I'm getting the following error during installation: ----- Proxy Error The proxy server received an invalid response from an upstream server. The proxy server could not handle the request POST /admin_toolshed/prepare_for_install. Reason: Error reading from remote server ----- In paster.log, I see this: ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 35420) Traceback (most recent call last): File "/galaxy/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib64/python2.6/SocketServer.py", line 332, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib64/python2.6/SocketServer.py", line 628, in __init__ self.finish() File "/usr/lib64/python2.6/SocketServer.py", line 671, in finish self.wfile.flush() File "/usr/lib64/python2.6/socket.py", line 303, in flush self._sock.sendall(buffer(data, write_offset, buffer_size)) error: [Errno 32] Broken pipe ---------------------------------------- Does this mean there's a problem on our side, or perhaps there is a file missing from the tool (or the connection to the Toolshed has a problem)? Any suggestions as to what I should look for? I first tried 2 days ago and waited until now to try again -- still the same problem. Thank you! Ray

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Auto-registration and database session issue
by Durdevic, Marija 06 Jun '16

06 Jun '16

Dear all, I am using LDAP authentication and auto registration options. LDAP authentication passed successfully, but I got error message during auto-registration process: File "/home/galaxy/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 450, in do_execute cursor.execute(statement, parameters) sqlalchemy.exc.IntegrityError: (psycopg2.IntegrityError) duplicate key value violates unique constraint "ix_role_name" DETAIL: Key (name)=(marija.durdevic(a)medunigraz.at) already exists. [SQL: 'INSERT INTO role (create_time, update_time, name, description, type, deleted) VALUES (%(create_time)s, %(update_time)s, %(name)s, %(description)s, %(type)s, %(deleted)s) RETURNING role.id'] [parameters: {'update_time': datetime.datetime(2016, 6, 6, 12, 43, 29, 93304), 'description': u'Private Role for marija.durdevic(a)medunigraz.at', 'deleted': False, 'create_time': datetime.datetime(2016, 6, 6, 12, 43, 29, 93290), 'type': 'private', 'name': u'marija.durdevic(a)medunigraz.at'}] [pid: 22823|app: 0|req: 2/2] 10.17.16.180 () {54 vars in 1129 bytes} [Mon Jun 6 14:43:29 2016] POST /user/login?use_panels=False => generated 0 bytes in 74 msecs (HTTP/1.1 500) 1 headers in 63 bytes (0 switches on core 1) After that, user appear in database and I am able to login. Anyhow, I would like to solve this issue and to register without errors. I tried to debug Galaxy code... It looks like that problem is somewhere with sessions... Script: Lib/galaxy/security/__init__.py Function: create_private_user_role( self, user ) In this line: self.sa_session.flush() Anny suggestion what can be wrong? Thanks in advance, Marija Mag. Marija Đurđević Core Facility Computational Bioanalytics Medical University of Graz Center for Medical Research Stiftingtalstraße 24, A-8010 Graz Austria Phone: +43 316/385-73024 Fax:+43 316/385-73009 Email: marija.djurdjevic(a)medunigraz.at Email: marija.djurdjevic(a)klinikum-graz.at Web: https://zmf.medunigraz.at/

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setting metadata externally failed for HistoryDatasetAssociation
by Anthony Underwood 06 Jun '16

06 Jun '16

Jobs that I run on a local Galaxy install on a Fedora 23 machine are completing but are erroring with the message below. Any idea why the metadata can not be written? Thanks galaxy.jobs.runners.local DEBUG 2016-06-03 17:30:02,044 execution finished: /home/anthony.underwood/galaxy/database/jobs_directory/000/142/galaxy_142.sh galaxy.model.metadata DEBUG 2016-06-03 17:30:02,158 setting metadata externally failed for HistoryDatasetAssociation 158: [Errno 2] No such file or directory galaxy.jobs.runners.local ERROR 2016-06-03 17:30:02,235 Job wrapper finish method failed Traceback (most recent call last): File "/home/anthony.underwood/galaxy/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/anthony.underwood/galaxy/lib/galaxy/jobs/__init__.py", line 1257, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/home/anthony.underwood/galaxy/lib/galaxy/datatypes/binary.py", line 339, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib64/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib64/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1335, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

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