galaxy-dev April 2014

galaxy-dev@lists.galaxyproject.org

91 participants
161 discussions

apache setting
by Jun Fan 12 May '14

12 May '14

Hi all, Following the instruction on https://wiki.galaxyproject.org/Admin/Config/ApacheProxy to use Apache as proxy for Galaxy, I got stuck to put directives into the configuration file. The steps I took include: 1. install apache2: sudo apt-get install apache2 2. install modules mod_proxy, mod_http_proxy and mod_rewrite to support proxying a. check if mod are already enabled using: apache2ctl -M b. install: sudo a2enmod rewrite, sudo a2enmod proxy, sudo a2enmod proxy_http 3. give galaxy permission to the apache user a. find out the user who runs apache: ps -ef | grep apache and find out it is www-data b. find out groups galaxy belong: groups galaxy => galaxy c. add user www-data to group galaxy: sudo usermod -a -G galaxy www-data I believe that I have completed the job required above the "Basic configuration" section. I tried the first example: RewriteEngine on RewriteRule ^(.*) http://localhost:8080$1 [P] I tried to add them to 1) the main conf file: apache2.conf, 2) newly generated httpd.conf by myself under /etc/apache2 folder and 3) newly generated .htaccess file under /etc/apache2/conf.d folder, and none of them gave me the luck. I used "sudo service apache2 restart" after every time I tried. There is a warning " Could not reliably determine the server's fully qualified domain name, using 127.0.1.1 for ServerName". When I type the address "127.0.0.1" or "127.0.1.1", both of them only gave me the default apache home page, not the Galaxy page. Of course the Galaxy is running on the same server. Could anyone give me some clue to continue? Best regards! Jun

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Portability and versionig in Galaxy
by Golestan (Sally) Radwan 06 May '14

06 May '14

Hi All, I am completely new to galaxy but part of my PhD research is to look at portability issues of workloads across different versions. I've tried looking at the wiki and the various pieces of documentation but no luck so far. Can someone please point me to a document or tutorial that explains how this is currently done in Galaxy and also any issues/gaps that may be worth addressing? I am also generally interested in how Galaxy works "under the hood". Is there a document that explains the architecture and design? Many thanks in advance! Sally.

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Help with cluster setup
by Jurgens de Bruin 02 May '14

02 May '14

Hi, This is my first Galaxy installation setup so apologies for stupid questions. I am setting up Galaxy on a Cluster running Torque as the resource manager. I am working through the documentation but I am unclear on some things: Firstly I am unable to find : *start_job_runners *within the universe_wsgi.ini and I dont want to just add this anywhere - any help on this would be create. Further more this is my job_conf.xml : <?xml version="1.0"?>  <job_conf> <plugins> <plugin id="hpc" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/> </plugins> <handlers> <!-- Additional job handlers - the id should match the name of a [server:<id>] in universe_wsgi.ini. <handler id="cn01"/> <handler id="cn02"/> </handlers> <destinations> <destination id="hpc" runner="drmaa"/> </destinations> </job_conf> Does this look meaning full, further more where to I set the additional server:<id> in the universe_wsgi.ini. As background the cluster has 13 compute nodes and a shared storage array that can be accessed by all nodes in the cluster. Thanks again -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin

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Re: [galaxy-dev] Galaxy Error Message
by Hans-Rudolf Hotz 02 May '14

02 May '14

"Please keep all replies on the list by using "reply all"" well, what happens if you run Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output on the command line yourself (or rather as the user galaxy is running as), replacing $genedata $pathwayid $species $output with meaningful arguments Hans-Rudolf On 04/28/2014 03:32 PM, Bradley Belfiore wrote: > Thank you for your quick response, my command tag is: > <command> > interpreter="bash">Rscript_wrapper.sh > /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata > $pathwayid $species $output > </command> > > So I believe Im calling R via the Rscript_wrapper.sh? > > As far as the #!/bin/bash, not sure why I had that there, I took it out now. > thanks, > Bradley Belfiore > > > On Mon, Apr 28, 2014 at 9:25 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch > <mailto:hrh@fmi.ch>> wrote: > > Hi Brad > > I don't you are using R to execute your R script.... > > How do you call your R script, ie how does the command tag looks in > the tool definition file? > > Also, why do you have a "#!/bin/bash" at the beginning of your R script? > > > Regards, Hans-Rudolf > > > > > On 04/27/2014 09:50 PM, Bradley Belfiore wrote: > > I am new to galaxy and while trying to convert an R tool to a Galaxy > usable tool I keep getting: > /Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1: > syntax > error near unexpected token `(' > > /Users/bmbelfio/galaxy-dist/__tools/pathview/pathview.R: line 1: > `args=(commandArgs(TRUE))' > > > any help as to how to remedy this would be greatly appreciated. The > first couple lines of my .R file are > # > #!/bin/bash > args<-(commandArgs(TRUE)) > > Thanks, > Brad > > > _____________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/__search/mailinglists/ > <http://galaxyproject.org/search/mailinglists/> > >

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purging deleted datasets
by Milad Bastami 02 May '14

02 May '14

Dear all,I have some unwanted datasets to remove but I need their main histories, so in galaxy I just deleted the unwanted datasets but not the histories. Then I tried to purge the deleted datasets with the following commands: python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 0 -6 -r python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 0 -3 -r and I saw the this error: /galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/types.py:215: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.Purged 0 datasetsFreed disk space: 0Elapsed time: 0.0748069286346 Unfortunately I can't understand the warning and why nothing was deleted. Any help would be most appreciated.

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Problem with the "set_library_permissions" function on bioblend
by Kevin Muret 30 Apr '14

30 Apr '14

Hello to all, In recent days, I try to do the "set_library_permissions ()" bioblend's function working. I tried the following syntaxes, and it was unsuccessful. Anybody know how to use it? Or otherwise,how would it be possible to modify user access to libraries (or contents)? ---------------------------------------------- Bonjour à tous, Depuis quelques jours, je tente de faire fonctionner la fonction "set_library_permissions()". J'ai tenté les syntaxes suivantes, et ce fût sans succès. Quelqu'un saurait-il comment l'utiliser ? Ou comment serait-il possible de modifier les accès utilisateurs d'une autre manière ? ---------------------------------------------- "instance" is opened with an admin API key. 1 --> print instance.libraries.set_library_permissions(library_id="417e33144b294c21", access_in=None, modify_in=None, add_in=None, manage_in=None) Traceback (most recent call last): File "Workflow_Lib/work_test.py", line 76, in <module> main() File "Workflow_Lib/work_test.py", line 39, in main print instance.libraries.set_library_permissions(library_id="417e33144b294c21", access_in=None, modify_in=None, add_in=None, manage_in=None) File "/home/gcc2013/lib/bioblend/lib/python2.7/site-packages/bioblend-0.4.3_dev-py2.7.egg/bioblend/galaxy/libraries/__init__.py", line 308, in set_library_permissions return Client._post(self, payload, url=url) File "/home/gcc2013/lib/bioblend/lib/python2.7/site-packages/bioblend-0.4.3_dev-py2.7.egg/bioblend/galaxy/client.py", line 181, in _post r = self.gi.make_post_request(url, payload=payload, files_attached=files_attached) File "/home/gcc2013/lib/bioblend/lib/python2.7/site-packages/bioblend-0.4.3_dev-py2.7.egg/bioblend/galaxyclient.py", line 99, in make_post_request r.status_code, body=r.text) # @see self.body for HTTP response body bioblend.galaxy.client.ConnectionError: Unexpected response from galaxy: 500: <html> <head><title>Internal Server Error</title></head> <body> <h1>Internal Server Error</h1> <p>The server has either erred or is incapable of performing the requested operation. <br/> </p> <hr noshade> <div align="right">WSGI Server</div> </body> </html> 2 --> print instance.libraries.set_library_permissions(library_id="417e33144b294c21", access_in=[admin_id], modify_in=[admin_id], add_in=[admin_id], manage_in=[admin_id]) 3 --> Moreover,are we supposed to view the content of this page?http://localhost:8080/api/libraries/417e33144b294c21/permissions ---------------------------------------------- Thank you in advance to the community for your help, Kevin MURET Intern at Station Biologique de Roscoff ABiMS platform

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May 2014 Galaxy News Update
by Dave Clements 30 Apr '14

30 Apr '14

Hello all, The May 2014 Galaxy Update Newsletter<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05> is out! There's a lot going on in the project and the community right now. The big news in the past month is the move from the Galaxy-User mailing list to Galaxy Biostar<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Galaxy_Biostar> for user support. This has been running for a week now, and has been very well received. The other big news is upcoming events. *Early registration for GCC2013 closes May 23 <https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#GCC2014:_June_30_-_Jul…>* . Register now <https://wiki.galaxyproject.org/Events/GCC2014/Register> and save more than 70% on registration costs, and Training Day<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> registration is an additional 55% off if you register for both at the same time. We are also pleased to announce this year's keynote speaker<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Keynote_Speaker:_Steve…> and the first ever GCC Hackathon<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Galaxy_Hackathon_at_GC…> . There's also a Galaxy UK Tour<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#UK_May_2014_Galaxy_Tour> which is visiting Norwich and Edinburgh in May, and there are at least 17 other Galaxy related events<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Other_Events> in the next 70 days in Norway, France, *online*, Croatia, Thailand, Canada, the US, the Netherlands, and Australia As always, there are new papers<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#New_Papers> (47 of them, including four we highlighted), new public Galaxy Servers<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#New_Public_Servers> (Globus Genomics Proteomics<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Globus_Genomics_Proteo…> and SunLab Galaxy<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#SunLab> ), new jobs<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Who.27s_Hiring> (7 postings in 6 countries), new tools in the project ToolShed<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#Galaxy_Project_ToolShe…> (um, *lots*), and a new public ToolShed<https://wiki.galaxyproject.org/GalaxyUpdates/2014_05#New_Public_Tool_Sheds> (at the Dutch Techcentre for Life Sciences (DTL) <http://www.dtls.nl/dtl/>. Dave Clements and the Galaxy Team<https://wiki.galaxyproject.org/GalaxyTeam> http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Test ToolShed package_samtools_0_1_19 status error?
by Peter Cock 29 Apr '14

29 Apr '14

Hi all, I'm working on a new wrapper for "samtools depad" (which I have been using with MIRA v4 output), now on the Test ToolShed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad The unit tests work for me locally and via TravisCI. The nightly ToolShed tests are failing - something seems to have gone wrong with the samtools dependency ("status Error") event though the samtools package is listed as a successful installation. Odd... Any thoughts? Thanks, Peter -- Automated tool test results Automated test environment *Time tested:* 2014-04-16 05:07:24 *System:* Linux 3.8.0-30-generic *Architecture:* x86_64 *Python version:* 2.7.4 *Galaxy revision:*13078:6f698dec5895 *Galaxy database version:* 118 *Tool shed revision:* 13018:e20408b06d65 *Tool shed database version:* 22 *Tool shed mercurial version:* 2.2.3 Installation errors Tool dependencies TypeNameVersion samtools package 0.1.19 Error This tool dependency's required tool dependency samtools version 0.1.19 has status Error. Successful installations Repository dependencies* - installation of these additional repositories is required* Tool shedNameOwnerChangeset revision testtoolshed.g2.bx.psu.edu package_samtools_0_1_19 iuc 36aa94676939

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disk space error
by Jess Gaunt 29 Apr '14

29 Apr '14

I hope this is the correct place to submit this problem. I'm using Galaxy main and there appears to be an error in the calculation of the disk space I'm using. I was using 7% of the allowed 250GB and then ran a series of jobs that produced files of ~200GB each. I deleted all of those jobs (most of which hadn't started execution), and then went back and deleted each one permanently, and my usage went back down to 7%. I requested a few jobs which should have produced smaller files, and they paused straight after starting. When I checked back, I was suddenly apparently using 597GB of disk space despite the size on disk of each of my histories adding up to <25GB. I've permanently deleted everything created since the initial problems and still my usage is recorded as 597GB. On Trello, there's a bug report that currently running jobs in deleted histories don't stop execution. Possibly my problem is due to the same bug, despite all the tasks being purged and not recoverable. I cannot do anything on Galaxy until my recorded disk space usage dips back under 100%. Can anyone help? Many thanks, Jessica Gaunt

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Re: [galaxy-dev] RE : Error with "get data" function
by Martin Čech 29 Apr '14

29 Apr '14

Hi Noémie, the special characters are probably in the file path, so some of your folders, or your file name or your computer user name may contain these and when our server gets that path he does not like it and throws an error. Like I said, it is a problem on our side but you can get around it by checking these. Martin On Tue, Apr 29, 2014 at 4:08 AM, DELRIEU Noemie < Noemie.DELRIEU(a)gustaveroussy.fr> wrote: > Hello Martin, > > Thanks for your answer ! I have tried cleaning the browser cache and I > have used another browser, but the problem persists... In fact, I clicked > on "get data" and I chose one file in my computer to download. > I didn't use the character "é" in my e mail adress but I take into account > your advice ! > > Best regards, > > Noémie > ------------------------------ > *De :* emulatorer(a)gmail.com [emulatorer(a)gmail.com] de la part de Martin > Čech [marten(a)bx.psu.edu] > *Date d'envoi :* lundi 28 avril 2014 22:18 > *À :* DELRIEU Noemie > *Cc:* galaxy-dev(a)lists.bx.psu.edu > *Objet :* Re: [galaxy-dev] Error with "get data" function > > Hello Noémie Delrieu, > > can you please describe the process in which the error happens? Do you > only click on 'get data' or do you also select from the sublist? Also try > cleaning the browser cache or using Galaxy with other browser to check on > the issue. > > thanks > > Martin > Galaxy Team > > > On Sun, Apr 27, 2014 at 1:18 PM, DELRIEU Noemie < > Noemie.DELRIEU(a)gustaveroussy.fr> wrote: > >> Hello, >> >> I contact you because I need some help with my galaxy account. I can't >> use function"get data" for 3 days. >> This number error appears : >> >> *GURU MEDITATION: #18e5fee395824913a0f27ff2063a0ead* >> >> >> The adress mail noemie.delrieu(a)gustaveroussy.fr is used for log in on >> server. >> >> >> Thank you. >> >> >> Best regards >> *, * >> >> >> Noémie Delrieu >> >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > >

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galaxy-dev April 2014