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

Galaxy-distribution (Nouvelle version)
by CHEBBI Mohamed Amine 26 Jul '12

26 Jul '12

Bonsoir, Une nouvelle version de Galaxy vient de sortir. D’après le Monsieur du maling list de Galaxy, les bugs de crash liés à l'utilisation du visualiseur Trackster devraient être résolus. Pourriez vous me dire vos recommandations à ce propos. Merci Amine

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Browser refresh and autoscaling
by Wolosh, Glenn 26 Jul '12

26 Jul '12

If I turn on autoscale via the cloud console page, autoscale shows turned off on page refresh. This occurs with both safari and firefox on a Mac. I have not tried other OS/Browser combinations. Where on the server is the autoscale configuration? I would like to see whether or not the console page is lying to me. Thanks. Glenn (Gedaliah) Wolosh Scientific Programmer IST/High Performance and Research Computing University of Medicine & Dentistry of New Jersey (UMDNJ) 185 South Orange Avenue, MSB, Room C-631 University Heights, Newark, NJ 07101 Phone: 973.972.9835 Fax: 973.972.7412 woloshgm(a)umdnj.edu<mailto:woloshgm@umdnj.edu>

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galaxy database has two tables missing
by Derrick Lin 26 Jul '12

26 Jul '12

Hi guys, Recently we have discovered there is a bug in the database dump utility. And we had used the same utility to migrate the galaxy mysql database once. That resulted the on the current galaxy database, two tables are missing: genome_index_tool_data tool_dependency I am wondering if there is a safe way to repair the database so that these two tables get added back? Regards, Derrick

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Non-Library input for workflows
by Sascha Kastens 26 Jul '12

26 Jul '12

Hi all, I wrote a script which executes a workflow via the API. I was wondering whether it is possible to use non-library input for the workflow. At the moment the script submits each data into a library and then uses this data as input: for step_id, ds_in in workflow[?inputs?].iteritems(): wf_data[?ds_map?][step_id] = {?src?:?ld?, ?id?:ds[?id?]} What I am seeking for is something like this: wf_data[?ds_map?][step_id] = {?src?:?local?, ?path?:?path/to/file?} Cheers, Sascha Kastens Project Manager GATC Biotech AG Jakob-Stadler-Platz 7 D-78467 Konstanz Phone: +49 (0) 7531-81604110 Fax: +49 (0) 7531-816081 Email: s.kastens(a)gatc-biotech.com http://www.gatc-biotech.com http://www.twitter.com/gatcbiotech http://www.facebook.com/gatcbiotech http://www.xing.com/companies/gatcbiotechag GATC Biotech AG Chairman Supervisory Board: Fritz Pohl Board of Directors: Peter Pohl, Thomas Pohl, Dr. Marcus Benz UID: DE 142 315 733 | Registration: Konstanz, HRB 1757 | Registered Office: Konstanz The information contained in this email is intended solely for the addressee. Access to this email by anyone else unauthorized. If you are not the intended recipient, any form of disclosure, reproduction, distribution or any action taken or refrained from in reliance on it, is prohibited and may be unlawful. Please notify the sender immediately. The content of this email is not legally binding unless confirmed by letter.

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Question about SNP calling
by shamsher jagat 25 Jul '12

25 Jul '12

Is there a work flow/ tutorial how to call SNP and get significant SNP followed by their annotation. Thanks

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configuring job runner for toolshed tools
by David Hoover 25 Jul '12

25 Jul '12

Is there a way to configure a tool downloaded from the toolshed depot to use a job runner other than the local runner? The tool_id for the toolshed tool isn't honored in universe_wsgi.ini the way the default tools are. Specifically, has anyone configured a toolshed tool to use drmaa instead of localhost? David Hoover Helix Systems Staff

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Fwd: Galaxy crach while visualization
by Chebbi Mohamed Amine 25 Jul '12

25 Jul '12

---------- Forwarded message ---------- From: Chebbi Mohamed Amine <chebbimamine(a)gmail.com> Date: 2012/7/18 Subject: Re: [galaxy-dev] Galaxy crach while visualization To: Jeremy Goecks <jeremy.goecks(a)emory.edu> Hello Jeremy! Thanks for your response. Yes the paster.log is not complaining. Excuse me where I can found the javascript log. In /var/log I haven't any file related to javascript.log. Thanks Amine 2012/7/17 Jeremy Goecks <jeremy.goecks(a)emory.edu> > Hello Amine, > > The paster log looks normal, and Postgre log is standard given the crash. > Was there anything out of the ordinary that you can spot in the paster log > and/or Javascript log in your Web browser? > > Thanks, > J. > > On Jul 17, 2012, at 6:53 AM, Chebbi Mohamed Amine wrote: > > Hello Galaxy team ! > > I have e strange problem whith my Galaxy trackster visualization . While > viewing bookmarked regions in my visualisation the whole > Galaxy process crashed and needed to be restarted, mainly when I use > Chrome browser. > > Above the Paster.log : > > xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET > /galaxy/tracks/data?chrom=chr19&low=1183972&high=1185154&mode=Auto&resolution=2.954022988505747&dataset_id=f4b17be90d9b3c9d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D > HTTP/1.1" 200 - " > http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, > like Gecko) Chrome/20.0.1132.47 Safari/536.11" > xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET > /galaxy/tracks/data?chrom=chr19&low=1182790&high=1183972&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D > HTTP/1.1" 200 - " > http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, > like Gecko) Chrome/20.0.1132.47 Safari/536.11" > xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET > /galaxy/tracks/data?chrom=chr19&low=1181609&high=1182791&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D > HTTP/1.1" 200 - " > http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, > like Gecko) Chrome/20.0.1132.47 Safari/536.11" > xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET > /galaxy/tracks/data?chrom=chr19&low=1183972&high=1185154&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D > HTTP/1.1" 200 - " > http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, > like Gecko) Chrome/20.0.1132.47 Safari/536.11" > xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET > /galaxy/tracks/data?chrom=chr19&low=1180427&high=1181609&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D > HTTP/1.1" 200 - " > http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, > like Gecko) Chrome/20.0.1132.47 Safari/536.11" > xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET > /galaxy/tracks/data?chrom=chr19&low=1181609&high=1182791&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D > HTTP/1.1" 200 - " > http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) > AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11" > xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET > /galaxy/tracks/data?chrom=chr19&low=1182790&high=1183972&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D > HTTP/1.1" 200 - " > http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, > like Gecko) Chrome/20.0.1132.47 Safari/536.11" > xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:37 +0200] "GET > /galaxy/tracks/data?chrom=chr19&low=814128&high=815310&mode=Auto&resolution=2.954022988505747&dataset_id=7710e7c5028b7c3b&hda_ldda=hda&filter_cols=%5B%22Score%22%5D > HTTP/1.1" 200 - " > http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, > like Gecko) Chrome/20.0.1132.47 Safari/536.11" > > PostgreSQL saw the crach : > > 2012-07-12 12:56:40 CEST LOG: could not receive data from client: > Connection reset by peer > 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection > 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection > 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:00:46.907 > user=user database=database host=server port=33106 > 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection > 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection > 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection > 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:03:45.206 > user=user database=database host=server port=42867 > 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:06:43.257 > user=user database=database host=server port=56383 > 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:04:22.120 > user=user database=database host=server port=42663 > 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:04:22.596 > user=user database=database host=server port=42656 > > > Thanks > Amine > ___________________________________________________________ > 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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.loc file for tophat
by Andre Gatorano 25 Jul '12

25 Jul '12

Which .loc file corresponds to tophat? I looked through the .xml file for the wrapper and it made no reference to any .loc file. -- Andre Gatorano 847-845-9284 University of California San Diego

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Populating tool select menu with database data? <code> tag deprecated
by Kohler Manuel 25 Jul '12

25 Jul '12

Hi, I have a question related to this Galaxy threads: http://dev.list.galaxyproject.org/Populating-tool-select-menu-with-database -data-tp4139069.html I implemented the example with the deprecated <code> tag which is working fine. But I do not invest time in a tag which might vanish soon. What is the replacement for this tag or how is the way it should be done? Here is what I want to do: My ultimate goal is to load fastq.gz files from an external Data Management System which I can connect via a JSON API. Here is the code which generates the menu shwon in the attached screen shot: Python code: import jsonrpclib server = jsonrpclib.Server('https://<myserver>/rmi-general-information-v1.json') sessionToken = server.tryToAuthenticateForAllServices(<user>, <password>) projects = server.listProjects(sessionToken) experimentType = 'HT_SEQUENCING' def getExperiments(): eList = [] experiments = server.listExperiments(sessionToken, projects, experimentType) for experiment in experiments: eList.append([experiment['code'], experiment['code'], False]) return eList The corresponding XML file calls the getExperiments() function: <inputs> <param name="experiment" type="select" label="Experiment:" help="select Experiment" dynamic_options="getExperiments()"/> <outputs> <data format="fasta" name="output" label="more foo" /> </outputs> <code file="openbis_get_dataset.py" /> Depending on the selection in the first drop down list (experiments) I want to show/fill a second list which shows a list of items which are in the selected experiment. Finally the fastq files should be listed. The structure is like this: *Experiment1 - Sample1 + fastq1.gz + fastq2.gz + fastq3.gz - Sample2 + fastq1.gz + fastq2.gz *Experiment2 - Sample1 + fastq1.gz I am on Galaxy r7148. If somebody could direct me in the right direction would be highly appreciated. Kind regards Manuel -- Manuel Kohler Center for Information Sciences and Databases (C-ISD) Department of Biosystems Science & Engineering (D-BSSE) ETH Zurich, Maulbeerstrasse (1078, 1.02), CH-4058 Basel, +41 61 387 3132

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Local instance is running way too slow!!!
by Di Nguyen 24 Jul '12

24 Jul '12

Dear All, I successfully install Galaxy onto my new MBP with 16Gb or Ram but when I tried to use Galaxy, it is painfully slow! The first test I did was to create Admin and import data (RNA-seq fastq, about 6Gb in size) into database and then history and it worked fine. The second test was to run fasqgroomer on this fasq and it took forever (3 hours+). Anybody got in idea of why it is so slow? Would it be possible that Galaxy was set up to run a single process instead of 8-core processor? If that is the case, how to fix it? Please help! Di Nguyen Postdoc, U of W, Seattle, WA

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