- galaxy-dev - lists.galaxyproject.org

Workflow outputs
by SHAUN WEBB 03 Nov '10

03 Nov '10

Hi, I have a suggestion regarding outputs from a workflow. The new feature that allows you to mark the shown outputs and hide the rest is a great idea but I wonder if this could be implemented at the run stage rather than the design stage as sometimes I require different outputs from the same workflow. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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server for galaxy
by Andreu Alibés 03 Nov '10

03 Nov '10

Hi, This one is for the people that have a Galaxy instance running on their institutes/companies, but probably not for the people running the main galaxy website: What would you say the requirements of Galaxy are in terms of disk space, cpu/memory, etc..? Thanks, Andreu -- -------------------------------------------- Andreu Alibés, PhD Bioinformatics Core & EMBL-CRG Systems Biology Unit Center for Genomic Regulation C/ Dr. Aiguader 88, 08003 Barcelona, Spain Phone: +34 93 316 0202 http://sites.google.com/site/aalibes

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Limited access tools
by Dave Walton 03 Nov '10

03 Nov '10

We are interested in making some of our tools only available to a subset of users. It looks to me like all galaxy tools are available to all galaxy users. We were thinking about patching our local galaxy to use the same roles that are used for data files for tools as well. Is this something others are interested in? Is this something that's already being worked on by the galaxy core team? (We'd hate to duplicate effort if someone is already doing this) Thanks, Dave

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Re: [galaxy-dev] trouble with authentication through Apache
by Ross 02 Nov '10

02 Nov '10

On Tue, Nov 2, 2010 at 10:48 AM, David Hoover <hooverdm(a)helix.nih.gov> wrote: > I tried a number of things, but the only one that works is a hack to the galaxy remoteuser.py script. > > I am authenticating with Kerberos, and this introduces a string in the HTTP_COOKIE variable Odd - according to http://onlamp.com/pub/a/onlamp/2003/09/11/kerberos.html?page=2 the Kerberos module is supposed to automagically set REMOTE_USER to the full userid (email and all)? That http_remote_user hack is sure ugly - there must be a better way? Looking at our setup for LDAP we have the user id in the uid attribute, so RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e works for us without all the other stuff suggested in http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy Any suggestions Nate? > newuser=[userid] > > So, in remoteuser.py, I match the alphanumerical characters of the userid and set HTTP_REMOTE_USER directly. > > $ diff remoteuser.py remoteuser.py.ORIG > 6d5 > < import re > 79,81d77 > < match = re.search('newuser=([0-9a-zA-Z]+)',environ['HTTP_COOKIE']) > < if match: > < environ['HTTP_REMOTE_USER'] = match.group(1) > > This is really bad, because every time galaxy is updated I will need to change this script. Ultimately, it would be better if galaxy could access the $REMOTE_USER variable like perl and mod_cgi do. > > David > > On Nov 1, 2010, at 8:55 PM, Ross wrote: > > David, > > Please feel free to write some notes to summarize what you've learned > about Kerberos and apache? > > If you could contribute what you have learned in a form that we could > use to improve the documentation - telegraphic notes or longer > narratives are always welcome - we'll make sure they're added to our > wiki to help future users. > > Thanks for using and helping us improve Galaxy! > > > > On Mon, Nov 1, 2010 at 5:43 PM, David Hoover <hooverdm(a)helix.nih.gov> wrote: >> Ah, well the documentation on the wiki is not entirely complete... >> >> I figured out that the REMOTE_USER is not passed when Kerberos is used to authenticate, so I figured out a roundabout way of doing it using HTTP_COOKIE instead. Quite brutal. It's very similar to the problem with mod_authnz_ldap. >> >> David >> >> On Oct 29, 2010, at 7:46 PM, Ross wrote: >> >> David, the section "Serving Galaxy at a sub directory (such as /galaxy) " >> in http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy >> might help? >> >> On Fri, Oct 29, 2010 at 5:32 PM, David Hoover <hooverdm(a)helix.nih.gov> wrote: >>> >>> Hi, >>> >>> I'm trying to set up a Galaxy mirror, and I'd like to authenticate via Apache. I can get Galaxy going when I don't authenticate. >>> >>> It's running on the same machine as the Apache server, listening on port 8081. >>> >>> I've added the mod_rewrite stuff from http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy, but I'm' still getting an 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. >>> >>> Please contact your local Galaxy administrator. >>> >>> Here's the block from our Apache configuration: >>> >>> <Location "/galaxy"> >>> AuthName "NIH Login -- all lowercase, not prefixed with NIH\!" >>> AuthType Kerberos >>> Krb5Keytab /etc/auth_kerb.keytab >>> KrbAuthRealm NIH.GOV >>> KrbMethodNegotiate off >>> KrbSaveCredentials off >>> KrbVerifyKDC off >>> Require valid-user >>> RewriteCond %{IS_SUBREQ} ^false$ >>> RewriteCond %{LA-U:REMOTE_USER} (.+) >>> RewriteRule . - [E=RU:%1] >>> RequestHeader set REMOTE_USER %{RU}e >>> </Location> >>> >>> RewriteRule ^/galaxy$ /galaxy/ [R] >>> RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L] >>> RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy/static/scripts/packed/$1 [L] >>> RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L] >>> RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L] >>> RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L] >>> RewriteRule ^/galaxy(.*) http://localhost:8081$1 [P] >>> >>> Any ideas? >> >> > > -- Ross Lazarus MBBS MPH Associate Professor, Harvard Medical School Director of Bioinformatics, Channing Laboratory 181 Longwood Ave., Boston MA 02115, USA. Tel: +1 617 505 4850

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trouble with authentication through Apache
by David Hoover 02 Nov '10

02 Nov '10

Hi, I'm trying to set up a Galaxy mirror, and I'd like to authenticate via Apache. I can get Galaxy going when I don't authenticate. It's running on the same machine as the Apache server, listening on port 8081. I've added the mod_rewrite stuff from http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy, but I'm' still getting an 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. Please contact your local Galaxy administrator. Here's the block from our Apache configuration: <Location "/galaxy"> AuthName "NIH Login -- all lowercase, not prefixed with NIH\!" AuthType Kerberos Krb5Keytab /etc/auth_kerb.keytab KrbAuthRealm NIH.GOV KrbMethodNegotiate off KrbSaveCredentials off KrbVerifyKDC off Require valid-user RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{RU}e </Location> RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8081$1 [P] Any ideas? David Hoover Helix Systems Staff http://helix.nih.gov

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Missing files in local galaxy
by Zhe Chen 29 Oct '10

29 Oct '10

Hi, I got some errors with my local Galaxy. IOError: [Errno 2] No such file or directory: '/usr/local/galaxy-python/galaxy_dist/tool-data/lastz_seqs.loc' IOError: [Errno 2] No such file or directory: '/usr/local/galaxy-python/galaxy_dist/tool-data/lastz_seqs.loc' IOError: [Errno 2] No such file or directory: '/usr/local/galaxy-python/galaxy_dist/tool-data/perm_color_index.loc' Looks like I am missing some files. Where I can download them? Thanks

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Galaxy not canceling cluster jobs
by Glen Beane 28 Oct '10

28 Oct '10

If we cancel a job within Galaxy it does not seem to cancel the cluster job on the back end. For example, if run the "Map with BWA" too and immediately decide I made a mistake and want to run it with different options I cancel the job in Galaxy but if I run "qstat" on our cluster I see that the job is actually still running, and the pbs_server log shows no attempt by the galaxy user to qdel the job. Is this expected behavior? I noticed there is a python function called "stop_job" in lib/galaxy/jobs/runners/pbs.py, so it seems Galaxy should be calling this if a user cancels a job in Galaxy. I've also notice that in "stop_job" there is a potential problem. After doing a little testing I've found this call to pbs_deljob would require that the galaxy user have "manager" privileges in TORQUE: pbs.pbs_deljob( c, str( job.job_runner_external_id ), 'NULL' ) Noticed that if you call pbs_deljob this way as a non-manager you'll see a message to the effect of "the -m option requires manager privileges". It seems the intention of passing 'NULL' to pbs_deljob as the message parameter is to not set a message, so manager privileges should not be needed (since Galaxy is only deleting its own cluster jobs). Changing the code to this allows it to be run sucessfully as a non-manager: pbs.pbs_deljob( c, str( job.job_runner_external_id ), "") -- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153

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Possible to define a datatype corresponding to a directory?
by Len Trigg 28 Oct '10

28 Oct '10

Hi all, I have just downloaded galaxy, got up and running with a local installation. I'd like to have a crack at integrating some of our tools into the system. To start off with, we use a data format that is actually a directory containing multiple (variable number of) files and subdirectories. Is it possible to define a datatype that treats this directory as a single object in terms of using it as tool inputs and outputs? It seems like I could define a datatype corresponding to a zipped version of the directory (and this would be useful for uploading), but once it's uploaded I don't want the tools to be packing and unpacking zipfiles all the time. Cheers, Len.

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Algorithms used in Galaxy
by Daniyal Kazempour 28 Oct '10

28 Oct '10

Dear Galaxy-Developer Team, my name is Daniyal Kazempour, I am a student of Bioinformatics (5th term) and an undergrad. scientist at the Max Planck Institute of Developmental Biology (Dept.4) in Tübingen. In our Genomics and Metagenomics seminar we have talked about Galaxy and ran into a question we could not find an answer to (at least pubmed and your website do not provide these information). In Galaxy it is possible to create a phylogentic tree out of the data from several BLAST results. Now the question that emerges is: What algorithm(s) is(are) used to create from several BLAST results the phylogenetic trees (or is there some rough description of it available where the principle of it becomes clear?). And as another question: What does the 'scaling' stand for ? (on phylogenetic trees a 100%----------0% is visible (are that some bias/error rates?)) Many thanks in advance for any hints and with best regards Daniyal Kazempour

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suppress screen messages in R
by Freddy 28 Oct '10

28 Oct '10

I am trying to include R modules in Galaxy. A few of the things I encounter: a) warnings: any warnings() message in R makes Galaxy stop! For R in the shell this means nothing. It simply warns you and that is all, there is no problem or error, just a potential problem with for example rownames in a data.frame which is usually not a big deal to the user. b) screen messages: this is for example the outcome of a boolean somewhere in the function you are then using in R. It simply outputs a vector with the outcome from a boolean somewhere in the function. However, for Galaxy this is enough reason to see this as an error! and thus: stops! (this happened with function image() when making pdf of array images) In principle this is wrong, because Galaxy should only stop in case of an error, not because of one of the above. Still, you do want to see screen output, cause it is helpful in the devel stage. How to go around this? And I think, the galaxy team will probably have to answer this one.

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