- galaxy-dev - lists.galaxyproject.org

Problem related to a job that "failed"
by Kelkar, Hemant 14 May '12

14 May '12

All, This question pertains to a local galaxy install where the jobs are being submitted to a cluster running LSF. I periodically get an error from a galaxy job ("Job output not returned from cluster") even though the job completes properly on the cluster. In researching this issue our systems administrator discovered that the error seems to be happening because of NFS caching. The problem is that the job finishes on the job node, but the Galaxy server doesn't see that reflected in the output file because of delays in the cache update in NFS. The only solution he discovered was turning the caching off on the file system. In our case it is not possible because it will lead to a performance hit that would be not acceptable on the shared cluster. Most other file systems on the cluster are "NFS" so moving the database/pbs folder to another file system is not an option. I generally work around the NFS cache issue but now it is leading to a second problem. Since the job appears to be in some failed state to galaxy (it shows up as red in history) I can't seem to use the output file (even though it is there and I can see it using the "eye" icon) to move to the next step. The file attribute is set right. I assume a possible solution may be to reset the "failed" flag on the history item. Would this need to be done in the database? Downloading and then re-uploading the result file (a 25+ GB SAM file in this case) may be a workaround but it is not very practical. Any ideas/suggestions? Thanks, Hemant

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Fwd: Running Galaxy behind apache2
by CHEBBI Mohamed Amine 14 May '12

14 May '12

---------- Forwarded message ---------- From: CHEBBI Mohamed Amine <chebbimamine(a)gmail.com> Date: 2012/5/11 Subject: Re: [galaxy-dev] Running Galaxy behind apache2 To: Nate Coraor <nate(a)bx.psu.edu> Hi! When I go to http://<ip> it displays: It works! This is the default web page for this server. The web server software is running but no content has been added, yet. Should I create a galaxy service file to enable the galaxy process restarting? 2012/5/11 Nate Coraor <nate(a)bx.psu.edu> > On May 10, 2012, at 4:23 PM, CHEBBI Mohamed Amine wrote: > > > Hi Galaxy team ; > > I'am trying to put Galaxy into a production environment behind apache2 : > > > > I followed the tuto in > http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy for putting galaxy > behind apache2 so I installed all the modules required (proxy-mod ; > rewrite_mod etc ) and I configured the apache2.conf like above : > > > > RewriteEngine on > > RewriteRule ^/static/style/(.*) /usr/local/appli/Galaxy/ > > Galaxy_dist/static/june$ > > RewriteRule ^/static/scripts/(.*) > /usr/local/appli/Galaxy/Galaxy_dist/static/sc$ > > RewriteRule ^/static/(.*) /usr/local/appli/Galaxy/Galaxy_dist/static/$1 > [L] > > RewriteRule ^/favicon.ico > /usr/local/appli/Galaxy/Galaxy_dist/static/favicon.ic$ > > RewriteRule ^/robots.txt > /usr/local/appli/Galaxy/Galaxy_dist/static/robots.txt$ > > RewriteRule ^(.*) http://localhost:8080$1 [P] > > > > I modified also the universe_wsgi.ini galaxy file by setting: host = > 0.0.0.0 to enable Galaxy binding to any available network. > > > > After restarting apache, when t type http://xx.xxx.xx.xx:8080 it > doesn't establish a connection.? > > Hi, > > If you access port 8080 directly, you'd be bypassing the Apache proxy and > going directly to Galaxy's built-in web server. Also, if you didn't > restart the Galaxy process after setting host = 0.0.0.0, it would still > only be listening on localhost. > > What happens if you go to http://<ip> without specifying a port number? > > --nate > > > > > Is there a configuration more to do? > > Thank you in advance > > ___________________________________________________________ > > 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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About the creation of a new folder
by Ciara Ledero 13 May '12

13 May '12

Hi all, I would just like to ask if it's possible to create a new folder (via script) in the galaxy-dist folder. Cheers, CL

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May 11, 2012 Galaxy Development News Brief
by Jennifer Jackson 11 May '12

11 May '12

Dear Galaxy Community, The May 11, 2012 Galaxy Distribution has been released at: http://bitbucket.org/galaxy/galaxy-dist/ Complete News Brief <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_05_11> *Highlights:* * *EMBOSS* tools and datatypes have now moved from the _/Galaxy distribution/_ <http://bitbucket.org/galaxy/galaxy-dist/> to the /Galaxy Main Tool Shed/ <http://toolshed.g2.bx.psu.edu>. * Tool Integration Tests <http://wiki.g2.bx.psu.edu/Tool%20Shed#Using_Galaxy.27s_functional_test_fram…>, Custom Tool Panel Configuration <http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_to…>, and Configurable Tool Output Locations <http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files>. * Improved Multiprocess Job Handling <http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scal…> and Enhanced OpenID <http://openid.net> Support. * GATK <http://www.broadinstitute.org/gsa/wiki> version 1.4, FreeBayes <http://github.com/ekg/freebayes>, Updated *Megablast* using NCBI BLAST+ <http://blast.ncbi.nlm.nih.gov/Blast.cgi>, Trinity <http://trinityrnaseq.sourceforge.net>, WormBase 2 <http://www.wormbase.org>, and IGB <http://bioviz.org/igb/index.html> external display. * Trackster <http://wiki.g2.bx.psu.edu/Learn/Visualization> upgrades include /strand coloring/, /interval datatype support/, and /tabix indexing/ (fast!!). * Updated *User Interface*, *Workflow-API* upgrades, and *Custom UCSC Display*. *http://getgalaxy.org* *new*: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist *upgrade*: % hg pull -u -r 17d57db9a7c0 /Thanks for using Galaxy!/ Jennifer Jackson Galaxy Team <http://wiki.g2.bx.psu.edu/Galaxy%20Team> http://galaxyproject.org

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POST and WSGI
by Nikolai Vazov 11 May '12

11 May '12

Hi, I am trying to set up Galaxy with an IdP. Yet, after the autentication, the SAML data coming via POST method to the WSGI (Galaxy) dissappears. I can only see it in a Firefox add-on, scrolling, but there is no way I can get hold of it in order to validate the users. Any idea how one can get environ[wsgi.input].body or similar in controllers/user.py finctions? Some global var with this? Thank you in advance Nikolay -- Nikolay Vazov, PhD Research Computing Centre - http://hpc.uio.no USIT, University of Oslo

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cloudman on ubuntu 12.04
by Jorrit Boekel 11 May '12

11 May '12

Dear list, I have tried to use cloudman on ubuntu 12.04 (with mi-deployment scripts). It didn't run very smooth. One of the issues seems to be that SGE depends on libc.so.6, which is not in the location where cloudman expects it. If not fixed yet, I'll create a pull request for the fix (two lines or so in sge.py). cheers, jorrit boekel

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Re: [galaxy-dev] [galaxy-user] default data for a tool
by alex 10 May '12

10 May '12

Hi, I would like to write my xmls in a way that reduces the amount of effort a casual guest user would require to try a tool from my local galaxy install. For example, in the remove_beginning tool I would like to set it up in a way that I could tell someone to do this: 1) go to the website that has my local galaxy install 2) click on the 'remove_beginning' tool from the left panel of the galaxy page 3) click on the 'execute' button to see how the tool works But right now they would have to somehow import data before they 'execute' the tool. In comparison, the Mobyle interface includes a "use example data" link corresponding to step 2.5) click the 'use example data' link near each field that requires data I am not an experienced galaxy user or administrator and I'm just wondering if there is anything like this in galaxy to make it simpler for casual users who are curious to see what the tool does with default data but not curious enough to go through multiple steps to import some example data. Alex On Thu, May 10, 2012 at 5:57 PM, Jennifer Jackson <jen(a)bx.psu.edu> wrote: > Hello Alex, > > Do you mean a default dataset (that a user can modify or never modify) or > default form entry data? > > If default form entry data, then you can use the <param> tag set with > "value", as described in this wiki: > http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cparam.3E_t… > > Looking at existing tools that have default form data can provide good > examples. For instance, the tool: > > galaxy-central / tools / filters / remove_beginning.xml > > See the content in <param value="X" /> line 5 below > > > 1 <tool id="Remove beginning1" name="Remove beginning"> > 2 <description>of a file</description> > 3 <command interpreter="perl">remove_beginning.pl $input $num_lines > $out_file1</command> > 4 <inputs> > 5 <param name="num_lines" size="5" type="integer" value="1" > label="Remove first" help="lines"/> > 6 <param format="txt" name="input" type="data" label="from"/> > 7 </inputs> > 8 <outputs> > 9 <data format="input" name="out_file1" metadata_source="input"/> > 10 </outputs> > 12 <tests> > 13 <test> > 14 <param name="num_lines" value="5"/> > 15 <param name="input" value="1.bed"/> > 16 <output name="out_file1" file="eq-removebeginning.dat"/> > 17 </test> > 18 </tests> > 19 <help> > > > Hopefully this helps. If not, write back, or even better, add in some > clarification and post a brand new question/thread to the > galaxy-dev(a)bx.psu.edu mailing list (the best list for development > questions): > http://wiki.g2.bx.psu.edu/Support#Mailing_Lists > > Jen > Galaxy team > > > On 5/10/12 12:12 PM, alex wrote: >> >> Hi, >> >> Is there a way to specify default data for a tool, maybe inside an xml? >> >> Alex >> ___________________________________________________________ >> 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/ > > > -- > Jennifer Jackson > http://galaxyproject.org

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Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
by Edward Hills 10 May '12

10 May '12

RE: The chat about NZ/AUS communication us here at Otago University (Dunedin, NZ) are very very keen for this. Please email us at edward.hills(a)otago.ac.nz if this does decide to take off :) Cheers, Ed

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Loc file configuration question
by Raja Kelkar 10 May '12

10 May '12

I have two questions that pertain to a local install of galaxy: 1. I have been having trouble getting the “fetch sequences” à “extract genomic DNA” tool to work. Can someone identify the specific *.loc file that needs to have the info about the location of the genome sequence files? I get the following error when I run the extract tool: *No sequences are available for 'hg19’, request them by reporting this error.* * * 2. What configuration file(s) need to contain locations for the gtf/gff files? Thanks.

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Error when exporting history to file
by Sarah Diehl 10 May '12

10 May '12

Hi all, I get the following error when I try to export a specific history to file: 10.1.5.190 - - [07/May/2012:18:01:08 +0200] "GET /history/export_archive HTTP/1.1" 500 - "http://galaxy.immunbio.mpg.de/" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/20111108 Fedora/3.6.24-1.fc14 Firefox/3.6.24" Error - <type 'exceptions.TypeError'>: <galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.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 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError: <galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file... Any help is greatly appreciated! Best regards, Sarah

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