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

Directories for input/output
by Fabian Kilpert 31 Jan '12

31 Jan '12

Hi @ all, some programs are using directories - not files - for input and output. I found only examples in the wiki describing how to set up a tool-xml using file parameters/variables. So my question is: What must I do, when the program only has an folder output parameter and puts all generated files in there? How do I have to configure the xml that galaxy keeps track of these files? Thanks, Fabian -- Dr. Fabian Kilpert Hochschule Bremerhaven An der Karlstadt 8 D-27568 Bremerhaven Alfred-Wegener-Institut für Polar- und Meeresforschung Polare Biologische Ozeanographie / Rechenzentrum Am Handelshafen 12 D-27570 Bremerhaven Tel.: +49 (0)471 4831 1656 E-Mail: Fabian.Kilpert[at]awi.de Web: www.awi.de

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LDAP authentification
by Sarah Maman 31 Jan '12

31 Jan '12

Hello, I'm trying to install galaxy on a apache server,and i have the same error message than David HOOVER when i tried to generate the authentification files. Thanks to David Hoover who gives me some helpful explanation. When i read the thread on gmod, it seems,that the problem is solved (http://gmod.827538.n3.nabble.com/trouble-with-authentication-through-Apache… <http://gmod.827538.n3.nabble.com/trouble-with-authentication-through-Apache…>) but I did not find the solution in my case. I use LDAP authentification and Galaxy is implemented on a VM. Could you please explain me how to solve it. I really need help. I modified universe file ( in galaxy-dist) and i created .htaccess file in galaxy-dist/ : * in universe_wsgi.ini: use_remote_user = True remote_user_maildomain = example.org <http://example.org> * in .htaccess file in galaxy-dist/ Directory : 1 <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#…> # Define Galaxy as a valid Proxy 2 <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#…> <Proxy http://localhost:8080> 3 <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#…> Order deny,allow 4 <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#…> Allow from all 5 <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#…> </Proxy> 6 <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#…> #!highlight apache 7 <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#…> <Location "/"> 8 <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#…> AuthType Basic 9 <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#…> AuthBasicProvider *ldap* 10 <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#…> Auth*LDAP*URL "*ldap*://server:389/ou=People,dc=example,dc=org?uid?sub?(objectClass=person)" 11 <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#…> Authz*LDAP*Authoritative off 12 <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#…> Require valid-user 13 <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#…> # Set the REMOTE_USER header to the contents of the *LDAP* query response's "uid" attribute 14 <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#…> RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e 15 <http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#…> </Location> with location, AuthBasicProvider and proxy competed But i have the error : Access to Galaxy is denied Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server. This is generally due to a misconfiguration in the upstream server. Thank you, and best regards Sarah Maman

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dadaset (file) visualization
by Alfonso Núñez Salgado 31 Jan '12

31 Jan '12

Hi, I'm new in galaxy, but i've made several installations in different distributions. At his moment I'm using RHEL 6.1 and I'm not able to visualize certain files. After uploading a SAM file I click on the file title and a preview of few lines appears whith the rest of the available options. When i click on the "eye" button nothing happen. If i try to download it, i do receive an empty file. This behaviour occurs with other file extension (BAM, HTML), but not whith others (FASTA, FASTAq) Using wget: wget "http://10.0.0.2:8090/galaxy/datasets/5969b1f7201f12ae/display/?preview=True" --2011-12-01 18:18:56-- http://10.0.0.2:8090/galaxy/datasets/5969b1f7201f12ae/display/?preview=True Connecting to 10.0.0.2:8090... connected. HTTP request sent, awaiting response... 10.0.0.2 - - [01/Dec/2011:18:18:56 +0000] "GET /galaxy/datasets/5969b1f7201f12ae/display/?preview=True HTTP/1.0" 200 - "-" "Wget/1.12 (linux-gnu)" 200 OK Length: unspecified [text/plain] Saving to: `index.html?preview=True.3' finaly index.html?preview=True.3 is an empty file, and obviously, no errors is displayed with any of the debugging options. I've done the same tests in other distributions and apparently every thing seems right Can any one of you get some light to this unexplainable black hole? -- ===================================== Alfonso Núñez Salgado Unidad de Bioinformática Centro de Biologia Molecular Severo Ochoa C/Nicolás Cabrera 1 Universidad Autónoma de Madrid Cantoblanco, 28049 Madrid (Spain) Phone: (34) 91-196-4633 Fax: (34) 91-196-4420 web: http://ub.cbm.uam.es/ =====================================

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howto create external_service_types ?
by Diego Mauricio Riaño Pachón 30 Jan '12

30 Jan '12

Hi all, I would like to add an AB 3500 Genetic Analyzer sequencer, a real time 500 Fasta machine and and Ion Torrent PGM to my external service types, and manage all sequencing requests via galaxy. Is there any guide about how to create the XMLs for new instruments in the external_service_types? Thanks a lot in advance. Best regards, Diego Riaño -- ___________________________________ Diego Mauricio Riaño Pachón Profesor Asistente Grupo de Biología Computacional y Evolutiva http://bce.uniandes.edu.co/ Departamento de Ciencias Biológicas Universidad de los Andes Bogotá D.C., Colombia Tel: +571 3 394949 Ext 2763 Bloque A Oficina 307

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job cleanup files drmout and drmerr not found
by Shantanu Pavgi 30 Jan '12

30 Jan '12

I see following warning messages in galaxy logs after a job finishes up. Does it mean something is misconfigured or a tool did not generate stdout and stderr files? {{{ galaxy.datatypes.metadata DEBUG 2012-01-30 11:52:07,345 loading metadata from file for: HistoryDatasetAssociation 7 galaxy.jobs DEBUG 2012-01-30 11:52:07,743 job 7 ended galaxy.datatypes.metadata DEBUG 2012-01-30 11:52:07,743 Cleaning up external metadata files galaxy.jobs.runners.drmaa WARNING 2012-01-30 11:52:07,806 Unable to cleanup: [Errno 2] No such file or directory: '/scratch/galaxy_personal_install_files/job_working_directory/000/7/7.drmout' galaxy.jobs.runners.drmaa WARNING 2012-01-30 11:52:07,807 Unable to cleanup: [Errno 2] No such file or directory: '/scratch/galaxy_personal_install_files/job_working_directory/000/7/7.drmerr' }}} -- Thanks, Shantanu

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Unix user account/connection and Galaxy connection
by Sarah Maman 30 Jan '12

30 Jan '12

Dear all, There is currently no link between an user ssh connection on his own account (own space on Unix) and the Galaxy connection. How to run Galaxy on an Unix user account? How to link the data storage system and the Unix user account (symlink?)? The goal is to not need to copy or move data. PS : Thanks a lot to David, Gordon, Brad, Christophe and Nate for your help on LDAP authentification. I always try to find a solution (Apache configuration). I will inform Galaxy list when I will find a solution. Thanks in advance, Sarah

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Error while uploading the files(uploaded by ftp) to galaxy
by Prashant Gupta 30 Jan '12

30 Jan '12

Hi, I have installed the galaxy on production server. I have uploaded the files I require through ftp and now when I try to add it to the history, it gives me error "This link may not be followed from within Galaxy". However, I checked when the same galaxy distribution installed locally, it works fine. Can you please help me with this. Regards Prashant

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a job running problem
by Theodore Zeng 30 Jan '12

30 Jan '12

Hi Guys, I have been trying to implement galaxy-dist on our new server for days. After adding a new tool into galaxy, a strange problem happened when I was testing some sample data. After clicking the execute button, new jobs were adding to the History panel, then they shows "job is currently running" immediately,. However, the jobs isn't running at all actually, ps PID shows that those jobs have not been running for a second. The process is wait there forever. What is stranger, after I shut down the galaxy for a restart, the process start to run quickly, and the results of sample running are perfect. I think that is probably caused the misconfiguration of galaxy job scheduler, but I still can't figure out the reason by myself after several days trying. Do you have any idea about such a problem? Thanks! Best, TZ

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Re: [galaxy-dev] Some eggs are out of date...Fetch failed (Mac OS X 10.6) ERRATA CORRIGE
by Nate Coraor 30 Jan '12

30 Jan '12

On Jan 30, 2012, at 1:46 PM, Lucilla Luzi wrote: > Thank you Nate for your reply!! :) > > This is what I got. > > $ python ./scripts/get_platforms.py > macosx-10.6-universal-ucs2 > > (just FYI, I run this command from the galaxy-dist folder that has a path like this one: > /Users/me/My_programs/Galaxy/galaxy-dist/ ) Okay, you should definitely be able to download prebuilt eggs for this platform. Have you tried running python ./scripts/fetch_eggs.py multiple times? > BTW; have you also noticed my message of 25th of January?) Yes, thanks for the extra info. --nate > > Thank you a lot!! > Lu > > > On 1/30/12 18:40 , Nate Coraor wrote: >> On Jan 24, 2012, at 4:16 PM, Lucilla Luzi wrote: >> >> >>> ERRATA CORRIGE: sorry :( >>> >>> $ echo $PATH >>> /System/Library/Frameworks/Python.framework/Versions/2.6/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin >>> >>> -------- Original Message -------- >>> Subject: [galaxy-dev] Some eggs are out of date...Fetch failed (Mac OS X 10.6) >>> Date: Tue, 24 Jan 2012 22:06:42 +0100 >>> >>> >>> Hi, >>> >>> I'm pretty new to Galaxy, at least to this side. >>> I'm sorry to bother you with my issue, that, I read, was quite extensively discussed previously, but even if I think to have followed >>> correctly the instruction and further suggestions, I'm still not able to overcome the problem. >>> >>> I'm trying to install a local instance of Galaxy on my MAC (OS X10.6.8) >>> My Python version is 2.6.1 and I just installed Mercurial 2.0.2 for MacOS X 10.6. >>> >>> FYI >>> >>> $ python --version >>> Python 2.6.1 >>> >>> --->> wrong <<---see above >>> $ echo $PATH >>> /Users/myName/System/Library/Frameworks/Python.framework/Versions/2.6/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin >>> >>> When I try to run the run.sh I get the error attached below. >>> Can you envisage a possible reason why I'm getting this error? >>> Sorry for the naive admission, but from the error message >>> I'm not even capable to understand which are the "missing eggs"... >>> >>> If I'd have ignored a previous post with the solution, I apologize in advance. >>> Thank you a lot for your attention. >>> >> Hi Lu, >> >> Could you provide the output of the following?: >> >> % python ./scripts/get_platforms.py >> >> Thanks, >> --nate >> >> >> >>> Lu >>> >>> ------------------ >>> $ sh run.sh >>> Some eggs are out of date, attempting to fetch... >>> Traceback (most recent call last): >>> File "./scripts/fetch_eggs.py", line 30, in <module> >>> c.resolve() # Only fetch eggs required by the config >>> File "/Users/myName/My_programs/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve >>> egg.resolve() >>> File "/Users/myName/My_programs/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve >>> return self.version_conflict( e.args[0], e.args[1] ) >>> File "/Users/myName/My_programs/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict >>> r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) >>> File "/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/pkg_resources.py", line 518, in resolve >>> raise DistributionNotFound(req) # XXX put more info here >>> pkg_resources.DistributionNotFound: numpy==1.6.0 >>> Fetch failed. >>> >>> >>> ___________________________________________________________ >>> 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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Multiple Workflows broken?
by Dave Walton 30 Jan '12

30 Jan '12

We just upgraded our Galaxy server last week to the one from change-set b258de1e6cea. We have several workflows that leverage the ability to select multiple input files, that in turn launches an instance of the workflow per input file. When I use these workflows, it now only runs a single instance of the workflow. Is this feature broken? Did we miss something in our upgrade? Is it by chance fixed in one of the releases that have come out over the last couple weeks? Thanks, Dave

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