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
2 years, 2 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?
>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>>
>
>
>
>
2 years, 10 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
3 years, 3 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,
3 years, 4 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.
3 years, 5 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
3 years, 8 months
Login problem with Galaxy instance
by Makis Ladoukakis
Hi I have some experience with setting up Galaxy instances but I came across a very peculiar issue when trying to setup the newest version.
While I am able to register as a new user when I try to login I get redirected to the home page without being logged in.
In the galaxy.ini is I disabled user_activation as I don't want a confirmation e-mail for new registrations, altered the host to 0.0.0.0 for network use and changed the port (which i opened up through the apache webserver)
Am I missing something?
Any help would be appreciated.
Kind regards,
Efthymios Ladoukakis
3 years, 8 months
Re: [galaxy-dev] validator type="empty_field" is not working within repeat tags
by Anmol Hemrom
Hi,
I was trying to enforce not to allow empty string as an input to text
field. It is working outside the repeat tags but not working within repeat
tags.
1) Working fine
<param name="input" type="text" label="Enter Name">
<validator type="empty_field"/>
</param>
2) Not Working within repeat tags.
<repeat name="test" title="Test">
<param name="input" type="text" label="Enter Name">
<validator type="empty_field"/>
</param>
</repeat>
Thanks
Anmol
On Fri, May 29, 2015 at 2:00 PM, Dave Clements <clements(a)galaxyproject.org>
wrote:
> Hi Anmol,
>
> The best place to post this question is the Galaxy Dev List <
> galaxy-dev(a)lists.galaxyproject.org>. You can also search to see if
> anyone has asked a similar question at
> https://galaxyproject.org/search/web/
>
> Thanks,
>
> Dave C
>
> On Fri, May 29, 2015 at 6:56 AM, <anmol.jh(a)gmail.com> wrote:
>
>> Hi,
>>
>> I was trying to enforce not to allow empty string as an input to text
>> field. It is working outside the repeat tags but not working within repeat
>> tags.
>> 1) Working fine
>>
>> <param name="input" type="text" label="Enter Name">
>> <validator type="empty_field"/>
>> </param>
>>
>> 2) Not Working within repeat tags.
>>
>> <repeat name="test" title="Test">
>> <param name="input" type="text" label="Enter Name">
>> <validator type="empty_field"/>
>> </param>
>> </repeat>
>>
>> Thanks
>>
>> Anmol
>>
>> _____________________________________
>> Sent from http://dev.list.galaxyproject.org
>>
>>
>
>
> --
> http://galaxyproject.org/
> http://getgalaxy.org/
> http://usegalaxy.org/
> https://wiki.galaxyproject.org/
>
3 years, 9 months
Rename output from a repeat
by Ulf Schaefer
Hi all
We frequently use the syntax below to rename outputs of workflows that
we run in batch. It is convenient to have sample names from fastqs
carried over to sams, bams, vcfs, etc.
#{input1 | basename}.bam
This does not seem to be working for inputs that are in repeats, e.g.
the VelvetOptimiser. Does anybody know if there is a syntax to make this
work, maybe
#{repeatname[0].input1 | basename}.bam ?
Thanks a lot for your help
Ulf
**************************************************************************
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 Public Health England, 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.gov.uk/PHE
**************************************************************************
3 years, 10 months
samtools dependency changes ?
by Wolfgang Maier
Dear all,
with older Galaxies (prior to latest_15.03 I think), you could satisfy
Galaxy's samtools dependence for indexing bam files by having a samtools
executable in tool-dependencies/samtools/default/bin (with the
tool-dependencies directory declared as tool_dependency_dir in
galaxy.ini of course).
Now (checked with latest_15.03 and .05), this is not working any more!
The executable will still be used during bam uploads, but not when a bam
file gets created by a tool.
The reason is that before the job runner (tested this with the local job
runner only) used to build the dependency shell command for dependency
'samtools' before finishing a job, but now the job wrapper finish method
fails because it naively expects to find samtools on $PATH.
Best,
Wolfgang
3 years, 10 months
