galaxy-dev April 2013

galaxy-dev@lists.galaxyproject.org

87 participants
164 discussions

Running jobs as real user and extra_file_path
by Louise-Amélie Schmitt 29 Apr '17

29 Apr '17

Hi everyone, I just wanted to ask how the extra_file_path is handled in case of job running as the real user since the file_path is only writable by the galaxy user. Any clue? Thanks, L-A

3 3

Upload issue in local installation
by Batsal Devkota 06 Feb '16

06 Feb '16

I installed galaxy locally in a linux server. However, I cannot upload the files (no matter how small, I have tried few kb size fasta files). When I try to upload, the link to the file shows up in the History and gets a new number (purple box). When I click on the link I get 'Dataset is uploading' forever. In the terminal window where I start galaxy, I get the following error report: 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /root/tool_menu HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:33 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:40 -0400] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://redhat:8080/root/tool_menu" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /tool_runner/upload_async_create HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/tool_runner/upload_async_message" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:34:04 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:34:08 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" The last line keeps going for ever... writes new line every 4 secs. I am stuck and don't know where to look. Please help. Batsal.

6 7

filtering a <param> of type 'data' so only one type is available
by Dan Tenenbaum 24 Oct '14

24 Oct '14

Hi, I have a tool wrapper with a <param> of type="data". Currently, this renders as a text box with a drop down list that has 52 items in it (the number of things I have in my history, I guess). I'd like to filter this list so that only some items in the history (in my case any item whose name ends with '.rda') are shown in this dropdown. It seems like maybe the 'format' parameter to the 'param' tag is what I want, but: 1) I tried format="rda" and that didn't seem to change anything. 2) "rda" is not in the datatypes.conf file which the documentation suggests is required? (.rda is an extension used for serialized R objects.) The tool I'm working on only accepts rda files as input and the reason I'm asking for this is that it is all too easy to accidentally feed it a file of some other type. If the dropdown could be filtered so that only items which will work with the tool are shown, that would be great. Is there a way to do that? Thanks, Dan

4 5

Workflow param error leads to template error
by Paul-Michael Agapow 19 Sep '14

19 Sep '14

Looking for pointers on what might be causing this problem: A user had a moderately complicated workflow that when run under certain parameter values results in a traceback that ends: Module workflow_run_mako:232 in render_body >> for ic in oc.input_step.module.get_data_inputs(): AttributeError: 'WorkflowStep' object has no attribute 'module' After some puzzling, I realized one of the parameters was outside the allowed range (a max on an integer param) and that Galaxy was trying to render "run.mako" flagging up the error but erroring out. Why Galaxy tries to call this non-existent member is unclear to me. Any insight or places I should start exploring? Galaxy version: various (started with an 6-month old one, upgraded to latest production to see if it would fix error, it didn't) Hosting OS: CentOS 6 ------ Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Health Protection Agency (UK) ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

3 3

Old Tool Shed URL http://community.g2.bx.psu.edu/ dead
by Peter Cock 29 May '14

29 May '14

Hello all, Either I made a typo in some old README files, or the old URL for the Tool Shed http://community.g2.bx.psu.edu/ has stopped working. Could this redirect to the current Tool Shed address http://toolshed.g2.bx.psu.edu/ please? Thanks, Peter

3 6

user specific access/options
by Jennifer Jackson 20 May '14

20 May '14

Hi Petr, I am going to forward your email to the galaxy-dev list so that the development community can offer comments/suggestions. Best, Jen Galaxy team On 8/30/11 2:27 AM, Petr Novak wrote: > Hi everybody, > I am developing the application on Galaxy server. One of the requirement > is to create user specific list of options. Is it possible to access > somehow $__user_email__ in <options> tag or in <conditional> ?. I did > not found documentation how to used cheetah in galaxy tool xml files but > from files provided with galaxy, cheetah is used only in <command> and > <config> tag. Is that rigth? If it can be used in any part of xml > definition file it would make much easier to generate xml dynamicaly > based on the $__user_email__ > Does anybody have an idea how to manage this problem? > Petr Novak > > > ___________________________________________________________ > 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://usegalaxy.org http://galaxyproject.org/Support

3 2

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

3 9

registration problem
by Wesley Schaal 23 Apr '14

23 Apr '14

Galaxy-Dev, I have a new galaxy installation under Linux. It's running as an Apache proxy (subdirectory) with authentication through galaxy (not apache). When trying to register a new user (which will be the administrator), the registration page declare success ("Now logged in as foo") but I am still just an anonymous user. If I try to login, it appears to succeed but I'm still anonymous. If I purposely enter the wrong password, the system complains as it should but I never get proper credentials. If I take away the Apache proxy configuration and run on the internal server, the problem goes away: I can login as expected and get the correct environment. The error is clearly here but I feel like I've followed the procedure written on the wiki. Specifically, Apache ----------- RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy(.*) http://localhost:8082$1 [P] # 8080 and 8081 are busy Galaxy --------- [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy [app:main] filter-with = proxy-prefix cookie_path = /galaxy Any idea of what might be wrong? Don't know if it matters but I'm using a MySQL database. I can see new users and it seems to work well enough to complain when bad passwords are entered. -- Wes

3 2

A new tool_data_table_conf.xml created under tool-data directory
by Derrick Lin 18 Jan '14

18 Jan '14

Hi guys, After installing the BWA from the Tools Shed, I find there is a new tool_data_table_conf.xml got created under tool-data directory. The file contains the entries of BWA's loc files. I believe the installed BWA still relies on the tool_data_table_conf.xml under galaxy root dir. Anyone can clarify what the one under tool-data dir is for? Regards, Derrick

3 7

FTP Problem: Users cannot see their uploads files.
by Misharl mon 08 Dec '13

08 Dec '13

Hi everybody, I have managed to get proftpd to work, it can connect to the galaxy sql database, and users can log to upload files in their directory. But there is a problem, when a galaxy user logs in the galaxy web platform, the user can't see his upload files since Galaxy doesn't have the rights to open the directory. How can i change the permissions in proftpd so that galaxy can open the user directory? Thanks in advance to all. Mish

4 17

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galaxy-dev April 2013