April 2011 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Error when trying to download workflow
by Jeremy Goecks 14 Apr '11

14 Apr '11

Hi Sarah, I created your workflow on my Galaxy instance and was able to export it successfully, so updating your Galaxy instance may solve your problem. If not, let us know and we'll take a closer look. Finally, please direct your questions to one of our mailing lists rather than individual galaxy developers for community and archival purposes; I've cc'd this one to galaxy-dev. Thanks, J. On Apr 7, 2011, at 8:00 AM, Sarah Diehl wrote: > Hi Jeremy, > > I encounter a similar error like the one already posted on the galaxy-dev list (http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003699.html) when trying to download a workflow. > > Were you able to find a solution or are you still working on it? I attached a screenshot of the workflow (like you also requested on the list). Let me know if I can provide you with any additional details to help with the debugging. > > Best regards, > Sarah > > > > 10.1.5.190 - - [07/Apr/2011:13:33:42 +0200] "GET /workflow/export_to_file?id=0ac5da8467dc9e07 HTTP/1.1" 500 - "http://solweb2.immunbio.mpg.de/workflow/export?id=0ac5da8467dc9e07" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.16) Gecko/20110322 file:///home/diehl/Pictures/Screenshot.png > Fedora/3.6.16-1.fc14 Firefox/3.6.16" > Error - <type 'exceptions.TypeError'>: 'WorkflowStep' object is unsubscriptable > URL: http://solweb2.immunbio.mpg.de/workflow/export_to_file?id=0ac5da8467dc9e07 > File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ > app_iter = self.application(environ, start_response) > File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ > return self.application(environ, start_response) > File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ > return self.application(environ, start_response) > File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ > body = method( trans, **kwargs ) > File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 74 in decorator > return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) > File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1078 in export_to_file > stored_dict = self._workflow_to_dict( trans, stored ) > File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1571 in _workflow_to_dict > step['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) > TypeError: 'WorkflowStep' object is unsubscriptable > <Screenshot.png>

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Ratings on Tool Shed broken?
by Peter Cock 14 Apr '11

14 Apr '11

Hi all, I had wondered why none of the tools on the Galaxy Tool Shed had a rating, and had assumed it was just that so far no-one had bothered. I have a new theory, it doesn't work? I just viewed Brad's "BAM to BigWig" tool, clicked on "Tool Actions" then "Rate Tool", and got: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Can anyone reproduce this? I've tried a couple of other tools and the same thing happens. Thanks, Peter

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Output file naming / dataset's label
by Tanguy Le Carrour 14 Apr '11

14 Apr '11

Dear Galaxy Team, I started using Galaxy few months ago. I'm now setting up my first "real" workflows. I would like to keep the name of my input file through the various steps as dataset's label, maybe also modify it a bit, and finally give a "proper" name to the result file downloaded. A simple example: 1) date-sample_name.gff3 --[step1]-> date-sample_name-step1.tsv 2) date-sample_name-step1.tsv --[step2]-> date-sample_name-step1-step2.txt 3 download date-sample_name-step1-step2.txt I've seen that I can use the 'label' attribute in the tool config "data" tag to do so. But I don't know how to access the ${input.label} (?) and how to modify it. I doesn't stop me using my workflows, but it would definitely help my users not to get lost when they use them. Best regards, Tanguy Le Carrour -- Tanguy LE CARROUR Functional Genomics Center Zurich ETH Zurich / University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland

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Galaxy's recent problems
by Dave Clements 13 Apr '11

13 Apr '11

Hello all, Galaxy has been ill recently due to disk space on the server filling up. In the short term we are working on freeing up space. In the longer term we are working on adding a quota system to limit how much space any one user can take, and we've also ordered a lot more disk. In the mean time, *please take a look at your saved histories and datasets and delete anything you no longer need*. This will greatly help us get through the current rough patch. In the longer term, you can also consider setting up your own local Galaxy instance, or running Galaxy on the cloud. See: http://getgalaxy.org/ https://bitbucket.org/galaxy/galaxy-central/wiki/cloud Thanks for your patience while we work this out, Dave C and the Galaxy Team -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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direct http links from galaxy
by Sarah Diehl 13 Apr '11

13 Apr '11

Hello, currently we are using Galaxy as our main data storage to try and keep as few duplicates of the data as possible. However, some of our biologists prefer to view their data for example in IGV. Due to the many files it is bothersome for them to download all the data to their own computer to display it (they are running out of disc space). IGV has the possibility to access data through an http link, but the download links in Galaxy don't work, because they do not have a file ending. So my question is: is there a way to get an http link from Galaxy that directly points to the file? Best regards, Sarah Diehl

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MySQL to PostgreSQL migration scripts available here
by Louise-Amélie Schmitt 13 Apr '11

13 Apr '11

Hello everyone I finally managed to finish my two scripts. It's kind of dirty coded (I'm not a Perl fan + I was in a hurry), but at least they worked for me. I could successfully transfer the data from an old MySQL Galaxy to my new PSQL Galaxy. Before running the scripts, you should already have run your new Galaxy instance so that the tables are properly created. Please note that the scripts will erase everything the target database might contain. It's aimed to make a 'clone' of the old database, not to merge both. Here is how to do the transfer: Requirements: DBD::mysql and DBD:Pg Perl modules 1: run galaxy-My2Pg.pl with the appropriate arguments (see the comments in the script's first lines) 2: start your Galaxy instance If the galaxy instance starts without throwing a fit, you can probably stop here. (I didn't have that chance though) Otherwise you most certainly have the wrong database version: 3: run sh manage_db.sh upgrade (to get the version right) 4: run galaxy-My2Pg_fix-seq.pl with the appropriate arguments blah, it will set the sequences at the right number since manage_db.sh seems to mess them up. Please note that even if it might work for some other databases, it was only tested on Galaxy, and I decline any responsibility if it doesn't work, throws data trhough the windows or blows your whole office up. You should back your data up beforehand in any case. Cheers, LA

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Re: [galaxy-dev] Apache configuration problem?
by Yu Wang 12 Apr '11

12 Apr '11

hi, sarah, sorry for the confusion. I did change those lines with my own directories. And the files are readable for others. Regards, Yu Yu Wang Office: Department of Plant Science Center for Life and Food Sciences Weihenstephan Technical University Munich Lehrstuhl für Pflanzenzüchtung Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt Technische Universität München Room 026, Emil-Ramann-Str. 4 (old: Am Hochanger 4) Tel: ++49 8161 71-4139 Lab: Lehrstuhl für Genomorientierte Bioinformatik Maximus-von-Imhof-Forum 3. Room OG-L 09 Tel: ++49 8161 71-2132 yu.wang(a)wzw.tum.de D-85354 Freising Germany

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Apache configuration problem?
by Yu Wang 12 Apr '11

12 Apr '11

Hello, I installed Galaxy on Fedora 13. Everything works fine at http://127.0.0.1:8080 Then I followed instruction from https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy. I add the following lines to httpd.conf: RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/nate/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/nate/galaxy_dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/nate/galaxy_dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/nate/galaxy_dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/nate/galaxy_dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] and changed universe_wsgi.ini with [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy [app:main] filter-with = proxy-prefix cookie_path = /galaxy I restarted Apache and Galaxy. At http://127.0.0.1:8080 everything works fine but at http://xx.xx.xx.xx/galaxy I got a scrambled page. Apache error log said "[Mon Apr 11 17:43:03 2011] [error] [client xx.xx.xx.xx] (13)Permission denied: access to /galaxy/static/style/base.css denied, referer: http://xx.xx.xx.xx/galaxy/root/tool_menu [Mon Apr 11 17:43:03 2011] [error] [client xx.xx.xx.xx] (13)Permission denied: access to /galaxy/static/style/tool_menu.css denied, referer: http://xx.xx.xx.xx/galaxy/root/tool_menu [Mon Apr 11 17:43:03 2011] [error] [client xx.xx.xx.xx] (13)Permission denied: access to /galaxy/static/scripts/jquery.js denied, referer: http://xx.xx.xx.xx/galaxy/root/tool_menu [Mon Apr 11 17:43:03 2011] [error] [client xx.xx.xx.xx] (13)Permission denied: access to /galaxy/static/scripts/galaxy.base.js denied, referer: http://xx.xx.xx.xx/galaxy/root/tool_menu " Can anyone point out what was configured wrong? Many thanks in advance. Best regards, Yu Wang Yu Wang Office: Department of Plant Science Center for Life and Food Sciences Weihenstephan Technical University Munich Lehrstuhl für Pflanzenzüchtung Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt Technische Universität München Room 026, Emil-Ramann-Str. 4 (old: Am Hochanger 4) Tel: ++49 8161 71-4139 Lab: Lehrstuhl für Genomorientierte Bioinformatik Maximus-von-Imhof-Forum 3. Room OG-L 09 Tel: ++49 8161 71-2132 yu.wang(a)wzw.tum.de D-85354 Freising Germany

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"fetch failed" error during first execution of run.sh
by Paul Cantalupo 12 Apr '11

12 Apr '11

Hello, I downloaded galaxy-central with the command "hg clone https://bitbucket.org/galaxy/galaxy-central". Then I changed directory to "cd galaxy-central/" and typed "sh run.sh". I got the following output: ..... Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/usr/local/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, in res olve egg.resolve() File "/usr/local/galaxy-central/lib/galaxy/eggs/__init__.py", line 195, in res olve return self.version_conflict( e.args[0], e.args[1] ) File "/usr/local/galaxy-central/lib/galaxy/eggs/__init__.py", line 226, in ver sion_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg. fetch ) File "/usr/local/galaxy-central/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.3.0 Fetch failed. (2812) sirius-pipas:/usr/local/galaxy-central $ What do I try now? I'm working in a Cygwin environment and my python version is 2.6.5. Thank you, Paul U. of Pitt

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Bioinformatics Open Source Conference (BOSC 2011)--Abstracts due April 18th!
by Brad Chapman 12 Apr '11

12 Apr '11

Only one week left to submit an abstract to BOSC 2011! We have two great keynote speakers lined up (Lawrence Hunter and Matt Wood) and session topics that include parallel and cloud-based approaches to bioinformatics, genome content management, and tools for next-generation sequencing. We'd love to hear about your Open Source bioinformatics project! The 12th Annual Bioinformatics Open Source Conference (BOSC 2011) An ISMB 2011 Special Interest Group (SIG) July 15-16, 2011, in Vienna, Austria http://www.open-bio.org/wiki/BOSC_2011 Important Dates: April 18, 2011: Deadline for submitting abstracts to BOSC 2011 May 9, 2011: Notifications of accepted abstracts emailed to corresponding authors July 13-14, 2011: Codefest 2011 programming session (see http://www.open-bio.org/wiki/Codefest_2011 for details) July 15-16, 2011: BOSC 2011 July 17-19, 2011: ISMB 2011 The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form. We invite you to submit abstracts for talks and posters. Sessions include: - Approaches to parallel processing - Cloud-based approaches to improving software and data accessibility - The Semantic Web in open source bioinformatics - Data visualization - Tools for next-generation sequencing - Other Open Source software In addition to the above sessions, there will be a panel discussion about "Meeting the challenges of inter-institutional collaboration". We are also working to arrange a joint session with one of the other ISMB SIGs. Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce a competition for three Student Travel Awards for BOSC 2011. Each winner will be awarded $250 to defray the costs of travel to BOSC 2011. All students whose abstracts are accepted for talks will be considered for this award. For instructions on submitting your abstract, please visit http://www.open-bio.org/wiki/BOSC_2011#Abstract_Submission_Information BOSC 2011 Organizing Committee: Nomi Harris and Peter Rice (co-chairs); Brad Chapman, Peter Cock, Erwin Frise, Darin London, Ron Taylor

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