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
5 years, 5 months
Re: [galaxy-dev] how to create users through Galaxy API?
by Martin Čech
Hi,
you specify username, password and email in the body (payload) of the POST
as Key:Value pairs.
Code from the API method: (
https://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/webapps/...)
username = payload[ 'username' ] email = payload[ 'email' ] password =
payload[ 'password' ]
There are also other conditions that need to be fulfilled (e.g. user
creation has to be turned on in the configuration) - you will find these
when you look at the source code of the method (because the documentation
is not perfect yet, sorry).
M.
On Sun, Dec 29, 2013 at 11:22 PM, xlwang <xlwang_0903(a)163.com> wrote:
> hi,
> I still have some confusion.
> post /api/users , when i use postman, it seems like this:
>
>
> No other parameters? How to confirm the new user's information?Such as
> user name, password.
> Can you give me a example please?Thank you!
>
> At 2013-12-30 06:04:15,"Martin Čech" <marten(a)bx.psu.edu> wrote:
>
> Hello,
>
> to create a user through API you send a POST request to /api/users
>
> More information about User API here:
>
>
> https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galax...
>
> Martin
>
>
> On Fri, Dec 27, 2013 at 5:11 AM, xlwang <xlwang_0903(a)163.com> wrote:
>
>> hello,
>> I want to create users through Galaxy API.For example, I can get users
>> information through url like this(use postman):
>> http://localhost:8080/api/users?key=my_key
>> But how to create a user?
>>
>>
>>
>> ___________________________________________________________
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>>
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>>
>
>
>
>
6 years, 1 month
tabular file displayed without tabs
by Ryan G
Hi - I have a tools that generates a tab-delimited text file as output.
when I click the eye icon to view the data, all the fields are compressed
as if there were no tabs. If I expand the history view, the little preview
window shows the contents as tabbed. I've verified that the spaces are
indeed '\t' tab characters. Why would Galaxy not display this file as a
tab-delimited file?
6 years, 3 months
not sure what I can do about this...
by Fernandez Edgar
Hello Gents,
So someone asked me to install the package Prokka on Galaxy.
I did and everything went well!
However, the following error comes up, when they try to work with Prokka:
Fatal error: Exit code 2 ()
[tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version.
[20:20:53] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.10 from http://www.vicbioinformatics.com' -Z outdir\/prokka\.err -i outdir\/prokka\.fsa 2> /dev/null
According to a google search, there is very little on this error.
And it has been around for a while but I didn't find a posted solution.
Any suggestions?
Cordialement / Regards,
Edgar Fernandez
System Administrator (Linux)
Direction Générale des Technologies de l'Information et de la Communication
* Bur. : 1-514-343-6111 poste 16568
Université de Montréal
PAVILLON ROGER-GAUDRY, bureau X-218
6 years, 3 months
Data removal after ftp import.
by Zuzanna K. Filutowska
Dear All,
is there any option to not remove files that has been imported to Galaxy
from FTP directory and to not remove files that haven't been imported
since 3 days?
--
Regards,
--
Zuzanna K. Filutowska, HPC Systems Administrator
Poznan Supercomputing and Networking Center
Institute of Bioorganic Chemistry Polish Academy of Sciences
Seize the day boys! Make your lifes extraordinary! --John Keating
6 years, 5 months
error loading files into galaxy
by Hakeem Almabrazi
Hi,
I started getting the following error whenever I try to load a file into Galaxy local.
Traceback (most recent call last):
File "/usr/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 8, in <module>
from galaxy import eggs
ImportError: cannot import name eggs
I will appreciate if someone can tell me what could happen to cause such issue and how to resolve it.
Regards,
6 years, 7 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.
6 years, 8 months
IOError kills collections
by Alexander Vowinkel
Hi,
when I run a tool on a big collection with cloudman,
I get the following error in at least one of the tasks:
Traceback (most recent call last):
File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/runners/drmaa.py", line
151, in queue_job
fh = file( ajs.job_file, "w" )
IOError: [Errno 11] Resource temporarily unavailable:
'/mnt/galaxy/tmp/job_working_directory/000/714/galaxy_714.sh'
What can I do here?
Also now the collection of the results is missing the
result of this collection element, correct?
How can I 'repair' my collection?
Thanks,
Alexander
6 years, 9 months
galaxy folder tree permissions
by lejeczek
hi everybody
I'd like to ask if you think it's worthwhile is pursuing
finely grained tree permissions? Would this improve security
to leave out everything but only files/folders necessary for
writing - to galaxy user what needs to write everything else
root?
Or just full perms to galaxy user on whole tree is the only way?
many thanks.
6 years, 10 months
list collection output - format set from input
by Alexander Vowinkel
Hi,
I have an input, that can be fasta,fastqsanger,fastqillumina:
<param name="fastq_input1" type="data"
format="fasta,fastqsanger,fastqillumina" label="Select the fastq file"
help="Specify fastq file with reads"/>
I have multiple outputfiles - bundled in a list collection:
<collection name="split_output" type="list" label="@OUTPUT_NAME_PREFIX@ on
${on_string} (Fastq Collection)" format_source="fastq_input1">
<discover_datasets pattern="__name_and_ext__" directory="splits" />
</collection>
The format_source parameter doesn't work - the files in the list (extension
fq) are of format "fq"
How can I make it possible that they are fasta,fastqsanger,fastqillumina
depending on fastq_input1?
Thanks,
Alexander
6 years, 10 months
