Hi John
Thanks for your reply.
I've copied your job_conf.xml.
Unfortunately, I've got an error when I ran run.sh:
galaxy.jobs DEBUG 2014-06-25 09:06:17,610 Loading job configuration from
./job_conf.xml
galaxy.jobs DEBUG 2014-06-25 09:06:17,610 Read definition for handler 'main'
galaxy.jobs
Probably the same way by which it keeps track of you when you are logged
in: setting a cookie in the browser. I didn't verify this, but that is how
basically all web services do it. If you clear the galaxy cookies I expect
you will end up in a new empty workspace.
On 25 June 2014 01:18, Melissa
Jan is correct, this is what Galaxy does.
-Dannon
On Wed, Jun 25, 2014 at 6:29 AM, Jan Kanis jan.c...@jankanis.nl wrote:
Probably the same way by which it keeps track of you when you are logged
in: setting a cookie in the browser. I didn't verify this, but that is how
basically all web
Dear Galaxy developers
I'm trying to allow users to upload file via FTP.
I've been to the tutorial website but as a beginner, I understand nothing...
https://wiki.galaxyproject.org/Admin/Config/UploadviaFTP?action=showredirect=Admin%2FConfig%2FUpload+via+FTP
I've configured the
Hi Janis,
that is not working and it is currently not clear if we will change it.
Please see the following Trello Card:
https://trello.com/c/NsLJv9la/61-clean-up-tool-shed-setup-actions
One of my project during the upcoming GCC hackathon is to implement a
setup_python_environment, like the R,
Dear all,
I noticed a strange behaviour in our local galaxy installation. First of all,
my universe_wsgi.ini contains retry_metadata_internally = False and
cleanup_job = always. The tool writes its output simply into the
job_working_directory and we move it via mv static_filename.txt $output
Hey Jens,
I have tried a few different things and I have been unable to
replicate the behavior locally.
Is this tool specific or configuration specific - i.e. do you see
this behavior only with a specific tool or do the concatenate datasets
tool experience this as well say?
If it is tool
Thanks John, now it works !
You look like a Galaxy professional. Maybe you can help me again ? I've made an
another topic about a FTP setting to upload large file. I've been to the Galaxy
wiki tutorials but I don't understand a lot ...
Pat
Date: Wed, 25 Jun 2014 07:49:36 -0500
Subject: Re:
Slightly off topic, but I would like to caution that if you want to be able to
ensure that your workspace is still available across time periods/browser
sessions on the public site, then you should most definitely use registered
accounts, as we will not be able to recover any lost anonymous
Thanks for the major update of the Freebayes wrapper, excellent!
I've run into two issues, however.
1) When using set allelic scope I get the following error:
Fatal error: Exit code 1 ()
freebayes: unrecognized option `--min-repeat-length'
did you mean --min-repeat-size ?
2) When using a vcf
Hi folks,
In Upload files to a data library form, seems like whatever valid path I
enter for linking to data on the server, even with galaxy as user and r
permissions on the folder and files - I get the invalid paths message after
submitting? The basic form info:
p.s. I do have allow_library_path_paste = True set in universe_wsgi.ini
Damion
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Solved. It was actually a file permissions thing on an ancestral folder. I
will add a trello card to suggest slightly better error reporting on this
though.
Regards,
Damion
Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for
Disease Control
655 West 12th Avenue,
I'd like to set the job_working_directory to the user's home directory.
I'm using an apache proxy with ldap authentication. I'm assuming I need to
strip the remote_user_maildomain off the user name to do something like...
job_working_directory = ~%user/galaxy_working_directory
Is this
Hi Qi,
thank you very much for you contribution.
I will try to get your patch to the correct person during the upcoming
Galaxy Conference.
Cheers,
Bjoern
Am 13.06.2014 17:29, schrieb Qi, Chuyang:
Hi all,
When installing and testing the cd-hit tool from jjohnson from the main galaxy
There is certainly no flag in Galaxy to allow this.
Even if you tried to hack it in - there would be some problems. Galaxy
writes out some files to that working directory before running the job
- so there would need to be more chown-ing and stuff happening at the
beginning of the job - probably
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