October 2010 - galaxy-dev - lists.galaxyproject.org

Integrating tools with variable inputs
by Branden Timm 04 Nov '10

04 Nov '10

Hi All, Is there any documentation on how to integrate tools that take a variable number of input files? We'd like to integrate a tool with the following command line syntax: tool-name <n input files> <n column names> output1 output2 Thanks! -- Branden Timm System Administrator Great Lakes Bioenergy Research Center btimm(a)glbrc.wisc.edu

2 1

Correction to docstring for Tool.build_param_dict
by Peter 03 Nov '10

03 Nov '10

Hi all, Here is a small fix to the docstring for Tool.build_param_dict. Peter diff -r 53d1fa98fa05 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Thu Oct 21 16:10:26 2010 -0400 +++ b/lib/galaxy/tools/__init__.py Fri Oct 22 13:32:31 2010 +0100 @@ -1333,7 +1333,7 @@ line. Each value is wrapped in a `InputValueWrapper`, which allows all the attributes of the value to be used in the template, *but* when the __str__ method is called it actually calls the - `to_param_dict_value` method of the associated input. + `to_param_dict_string` method of the associated input. """ param_dict = dict() # All parameters go into the param_dict

2 1

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

3 6

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

5 4

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

2 1

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.

4 8

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

2 1

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.

6 7

[patch] unused tophat parameters
by Ry4an Brase 28 Oct '10

28 Oct '10

We had a sharp-eyed researcher notice that her tophat output with various parameters was always yielding the same results. JJ tracked it down to a bug in tophat_wrapper.py where the segment-length and segment-mismatches are displayed in the options and are parsed in ophat_wrapper.py, but those options are never added to the actual command line for tophat. Attached is a patch that wires them up. -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institute http://www.msi.umn.edu

2 1

A wierd horizontal line in the middle of tool
by Zhe Chen 28 Oct '10

28 Oct '10

Hi, In my local Galaxy, I have a horizontal line in the middle of the tool UI. How can I fix it? Picture attached. Thanks

1 1