May 2014 - galaxy-dev - lists.galaxyproject.org

Default value for data_column not working?
by Peter Cock 14 May '14

14 May '14

Hi all, I'm trying to write a new tool working with tabular data (specifically a Reciprocal Best Hits (RBH) tool using BLAST style tabular output). I want the user to be able to choose a column number (from one of the input files), but I have a default column in mind. However, Galaxy doesn't seem to obey the default column number: <inputs> <param name="a_vs_b" type="data" format="tabular" label="Hits from querying A against B" description="Tabular file, e.g. BLAST output" /> <param name="b_vs_a" type="data" format="tabular" label="Hits from querying B against A" description="Tabular file, e.g. BLAST output" /> <param name="id1" type="data_column" data_ref="a_vs_b" multiple="False" numerical="False" value="1" label="Column containing query ID" help="This is column 1 in standard BLAST tabular output" /> <param name="id2" type="data_column" data_ref="a_vs_b" multiple="False" numerical="False" value="2" label="Column containing match ID" help="This is column 2 in standard BLAST tabular output"/> <param name="score" type="data_column" data_ref="a_vs_b" multiple="False" numerical="False" value="12" label="Column containing containing score to rank on" help="The bitscore is column 12 in standard BLAST tabular output"/> </inputs> I've tried giving the default column value numerically (as shown), and also using value="c2" etc. Regardless, Galaxy just defaults to the first column. Is this a bug, or am I doing something wrong? Thanks, Peter

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Genomespace Integration with workflows
by Nuwan Goonasekera 14 May '14

14 May '14

Hi, This is with regard to a modification we'd like to propose for improving Genomespace integration with Galaxy, and we'd like to get some feedback from the core Galaxy devs. We are happy to make the changes and issue a pull request. The proposal is: 1. Allow the Genomespace Importer to be workflow compatible (that is, allow the Genomespace Importer to be dragged/dropped onto the workflow canvas and when the user attempts to run the workflow, provide a way to specify/browse for a file stored in Genomespace through a popup window) 2. Do the same for the Genomespace Exporter, so that, at the end of running a workflow, the file would be archived back in Genomespace automatically. So far, the only solid approach we've found to implement this is to introduce a new tool parameter (e.g. GenomespaceFileParameter, analogous to FtpFileParameter). It removes many of the constraints that the current genomespace import/export tools are bound by. It may also necessitate the inclusion of some javascript so that the file browse dialogue can be opened. Alternatively, it could be made more generic, e.g. CustomFileParameter instead of GenomespaceFileParameter - with a property for specifying a custom javascript handler. However, since tools do not appear to have a way of introducing custom javascript code at present, this approach may not be viable. So we were wondering whether the initial approach was alright or whether there's a better method of achieving this? Thanks /Nuwan

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backtrace from set_dataset_sizes.py
by Langhorst, Brad 13 May '14

13 May '14

python scripts/set_dataset_sizes.py Loading Galaxy model... Processing 134520 datasets... Completed 0% Traceback (most recent call last): File "scripts/set_dataset_sizes.py", line 43, in <module> dataset.set_total_size() File "lib/galaxy/model/__init__.py", line 1257, in set_total_size if self.object_store.exists(self, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True): AttributeError: 'NoneType' object has no attribute ‘exists' I’m seeing some odd sizes in galaxy, so I thought I’d attempt to re-initialize them. Is this expected to work? Brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist

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Keeping a tool from running multiple times at once
by Guillaume Penderia 13 May '14

13 May '14

Hi, I am currently working on a workflow with some custom tools, and one of these tools has to create very big temporary files (like 45Go big). As this workflow will be used on a lot of file at the same time, I have to keep it from running more than once or twice at the same time (the other execution would wait in the queue). If I don't, I'm afraid that some memory lack or something could cause all the executions to fail and stop. The problem is : I can't find if it's possible to do that, and if it is, how do I do it. Anyone has an idea please ?

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user account activation
by Jun Fan 12 May '14

12 May '14

Dear all, Has anyone got the problem of enabling user account activation recently? In the past, after setting user_activation_on = True in the universe_wsgi.ini, when I click "Analyze Data", a login window will appear to force me to log in. Now I can upload file without login and the green status showed in the history. When I tried to register a new user, the grey status of the upload tool appeared. I did receive the activation email. Best regards! Jun

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history item status not updating
by Robert Baertsch 12 May '14

12 May '14

I submitted a workflow that in turn submits a drm job to sun grid engine. The queue had an error (probably due to a problem with automount). Traceback (most recent call last): File "/inside/depot4/galaxy/lib/galaxy/jobs/runners/__init__.py", line 60, in run_next method(arg) File "/inside/depot4/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 169, in queue_job external_job_id = self.ds.runJob(jt) File "/inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/__init__.py", line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File "/inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/helpers.py", line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer)))) File "/inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/errors.py", line 90, in error_check raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value)) DeniedByDrmException: code 17: error: no suitable queues When the sysadmin cleared the error, the job started running normally after being in an error state for 10 minutes. The cool thing is that galaxy kept running without a problem. galaxy.jobs.runners.drmaa DEBUG 2013-06-27 14:51:22,968 (10481/4767487) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2013-06-27 15:00:23,628 (10481/4767487) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2013-06-27 15:00:27,751 (10481/4767487) state change: job is running However in the history panel, the job shows as queued but not running, even if I refresh the history panel. Is this normal or should the status change to running? I'm using this version of straight galaxy: changeset: 10162:f295092476c7 branch: stable parent: 10160:2efb1083676b user: Dannon Baker <dannonbaker(a)me.com> date: Sat Jun 15 09:08:09 2013 -0400 summary: Fix reports import issue reported by Lance, https://trello.com/card/bug-in-reports-webapp-imports/506338ce32ae458f6d15e… -Robert Baertsch UC Santa Cruz

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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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[GSoC2013] Nested Workflows for Galaxy
by Saket Choudhary 11 May '14

11 May '14

Hi all, I was a Google Summer of Code Student for Galaxy Project for the year 2013. One of my main tasks was to implement 'nested workflows' for Galaxy. See [1] This took me more time than I had expected and after sending a declined PR(See [2]) I re-attempted something similar with PR# 370. Through, few off-the-list discussions it has been decided that #370 would be declined as well. However, since this was a feature that was 'in-demand', I thought I would share it here, if in any case somebody finds it useful. The code is here[4]. However 'galaxy-central' is soon going to have a similar feature implemented soon and as such my code might not turn out to be so useful. However if you happen to find this useful and come across any bug(s) (apart from that listed on the PR) please feel free to report it. Thanks, Saket [1] https://trello.com/c/d4Onll9T/737-nested-workflows-or-workflow-modules [2] https://bitbucket.org/galaxy/galaxy-central/pull-request/229/nested-workflo… [3] https://bitbucket.org/galaxy/galaxy-central/pull-request/370/nested-workflo… [4] https://bitbucket.org/saketkc/galaxy-central-additions

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Re: [galaxy-dev] Inform tool interface with data specific to selected dataset
by Dooley, Damion 09 May '14

09 May '14

Hello, Eric, If the dynamic filters approach doesn't work out I can send you an approach that worked for me. It involves creating a tool-generated html report that contains a form which provides selection choices; and the form is set to submit to a 2nd tool of your choice tool (it contains the necessary fields to prime the tool). Not sure if it works on every breed of galaxy out there though. d.

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Inform tool interface with data specific to selected dataset
by Eric Rasche 09 May '14

09 May '14

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