Running jobs as real user and extra_file_path
by Louise-Amélie Schmitt
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 years, 8 months
Upload issue in local installation
by Batsal Devkota
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.
4 years, 11 months
Workflow param error leads to template error
by Paul-Michael Agapow
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)
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6 years, 4 months
user specific access/options
by Jennifer Jackson
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
6 years, 8 months
Default value for data_column not working?
by Peter Cock
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
6 years, 8 months
FTP Problem: Users cannot see their uploads files.
by Misharl mon
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
7 years, 1 month
Compressed data files in Galaxy? (e.g. GZIP or BGZF)
by Peter Cock
Hello all,
What is the current status in Galaxy for supporting compressed files?
We've talked about this before, for example in addition to FASTQ,
many of us have expressed a wish to work with gzipped FASTQ.
I understand that some have customized their local Galaxy
installations to use gzipped FASTQ as a specific data type - I'm
more interested in a general file format neutral solution.
Also, I'd like to be able to used BGZF (not just GZIP) because it
is better for random access - see for example
http://blastedbio.blogspot.com/2011/11/bgzf-blocked-bigger-better-gzip.html
- and makes it much easier to break up large datafiles for sharing
over a cluster (i.e. it could be exploited in the current Galaxy code
for splitting large sequence files).
The 11 May 2012 Galaxy Development News Brief
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-May/009757.html
mentions tabix indexing - that uses bgzip, so is there something
general in place yet to allow tool wrappers to say they accept not just
given file formats, but different compressed versions of file formats?
Ideally I'd like to be able to write an XML tool description saying
a tool produced BGZF compressed tabular data, or GZIP
compressed Sanger FASTQ etc. Similarly, I'd like to specify my
tool accepts FASTA or gzipped FASTA (including BGZF FASTA).
While for older tools if they say they accept only uncompressed
FASTA, Galaxy could automatically decompress any compressed
FASTA entries in my history on demand.
Peter
7 years, 1 month
Re: [galaxy-dev] [galaxy-user] Inquiring
by Nate Coraor
Hi Yan,
I've moved this discussion to the galaxy-dev list since it pertains to a
local installation of Galaxy.
Responses to your questions follow, in-line.
Yan Luo wrote:
> Dear Sir,
>
> (1)We installed Galaxy, but recently the user can't registered and got the
> following error, how can we fix it?
>
> Sever error
> An error occurred. See the error logs for more information.(To turn debug on
> to display ...).
Since debug = False in universe_wsgi.ini, you should be able to find a
more detailed error message in the log file. If starting Galaxy with:
% sh run.sh --daemon
The default log file is 'paster.log' in Galaxy's root directory.
> (2) Could you please let me know if there is any command to stop galaxy?
If starting with the --daemon flag (as above), you can use:
% sh run.sh --stop-daemon
If running in the foreground, you can use Ctrl-C to terminate the
process. There is a recent bug whereby Ctrl-C is ineffective on some
platforms under Python 2.6 - in this case you will have to kill/pkill
the process manually. We are working on a fix for the latter.
> (3) If I reset universe_wsgi.ini file and want to set an administrator
> user(I can add a line in the above file), how can I get the password? Should
> I stop galaxy(See question 2) first? then run "./setup.sh" and "./run.sh".
setup.sh would have only been necessary prior to running Galaxy the
first time, however, this step has recently been removed. If you are
referencing documentation that still refers to setup.sh, please let us
know so we can update it - I did notice this was still on the
"Production Server" page, so I removed it from there.
You no longer need to run setup.sh at all.
> (4) If I run "setup.sh", will a new file "universe_wsgi.ini" be generated?
> if I want to change this file,should I edit it before "run.sh" and after
> "setup.sh". Is it right?
setup.sh and its replacements in run.sh and the Galaxy application
itself never overwrite files, they only create files from sample files
if they do not exist.
> (5) I read some of your docs, command "sh setup.sh"(sh run.sh) and
> "./setup.sh"(./run.sh), which one is correct under Linux?
Both syntaxes are effectively the same in most cases.
--nate
>
> Looking forward to hearing from you.
>
> Best Wises,
>
> Yan Luo, Ph.D.
> NIH
> <http://int.ask.com/web?siteid=10000861&webqsrc=999&l=dis&q=By%20the%20way,>
> _______________________________________________
> galaxy-user mailing list
> galaxy-user(a)lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-user
7 years, 2 months
samtools BAM to SAM tmp directory
by Matt Shirley
Is there a reason that the samtools BAM to SAM does not respect the
new_file_path set in the config file? The tmp directory handling by
different tool wrappers seems to be an issue right now on systems with
small system tmp directories.
--
Matt Shirley
Ph.D Candidate - BCMB
Pevsner Lab <http://pevsnerlab.kennedykrieger.org/>
Johns Hopkins Medicine
7 years, 6 months
Displaying genomic sequences in Trackster
by Naharajan Lakshmanaperumal
Dear all,
We have our own galaxy instance and the idea is to have trackster enabled for users to be able to visualize NGS mapping. We were able to configure trackster in our instance and the visualization works fine.
We have two questions regarding trackster:
1) We can't display genomic sequences in trackster. As per the tutorial, we set the location of the .2bit file in the twobit.loc file for the trackster to be able to display the genomic sequence but for some reason it doesn't display it. The name of the builds is the same in all places i.e) in ucsc/chrom/builds.txt and also in the .loc files. Any ideas on what else should be done?
2) While saving the visualization, there is always an error message saying "could not save visualization" and it doesn't seem to be a web browser issue. How do we then save the visualization?
Thanks in advance,
Naharajan
7 years, 8 months
