Hi Shane,
We had enabled this feature on our cluster working with PBS but since we
switched to LSF, we never managed to have it working again. Same error as yours
if I correctly remember. After hours spent looking into LSF, I think we
understood that LSF somehow catches the user change and
Dear Galaxy developers,
The University of Oslo is in the process of hiring a system developer that will
partly work on Galaxy-based infrastructure in the context of the ELIXIR
infrastructure project, and partly as a developer of the Genomic HyperBrowser
and related Galaxy-based analysis
Hi Galaxy devs,
We're deploying Galaxy on the Michigan State HPCC and doing it as a hack-a-thon
today.
Our authentication is Shibboleth and our scheduler is Torque/Moab, and we're
setting it up with 'run as user' with a shared file space /mnt/research/galaxy
To set up we've installed base
Hello,
does anybody have any idea of what I can do to fix the problem?
Maybe an update is required? I currently use the changeset:
11219:5c789ab4144a
thanks
Yec'han
Dr. Yec'han LAIZET
Ingenieur Bioinformatique
Tel: +33 (0)5 57 12 27 75
Would it be possible that you have an old copy of the bx-python egg? You should
have bx-python 0.7.1
If you check your eggs directory and you see version 0.7.1, then there may be
something wrong with bx-python. In this case, please upload your build and bam
to our public server and try
Hi Ravi,
I checked and the bowtie2 tool repository had a misconfigured data table name
in its tool_data_table_conf.xml.sample file that was erroneously creating a
tophat2_indexes data table, whereas the tool itself uses bowtie2_indexes.
Can you try to uninstall and reinstall bowtie2 from the
Greetings,
Since yesterday, I have been experiencing an unusual problem with Uploading
files.
Seemingly at random, an uploaded will finish successfully (history item in
green) but no preview is available. Under the title of the item, the keyword
empty is found and preview box says no peek.
Greetings,
I and another individual are attempting to test Galaxy's ability to share data.
We have attempted to share histories and workflows, selecting only each other's
user email address for people to allow sharing with.
All cases have failed, we go to the Shared Data section in both
Hi Ravi,
To view histories shared with you, click on the history options (gear icon in
the right) and click “View Histories Shared with Me”. To view shared workflows,
go into the workflow interface and scroll down to the “Workflows shared with
you by others”. Please let us know if that doesn’t
Hi Dan,
Yes, we see them now. Thank you.
--
Ravi Sanka
ICS – Sr. Bioinformatics Engineer
J. Craig Venter Institute
301-795-7743
--
From: Daniel Blankenberg d...@bx.psu.edumailto:d...@bx.psu.edu
Date:
Hi Ravi,
The directory structure for the installation of ToolShed tools changed,
which is why you have three directories. You perhaps had bowtie2
installed once before, then reinstalled (without completely removing the
older version and associated data)? Or updated without resetting the
Hi Charles,
That actually helps. I don't have any choice in running LSF but knowing that
it didn't work because LSF is rejecting it helps when I talk to my boss about
why I couldn't do it.
Shane
On 5/03/2014, at 10:28 pm, Charles Girardot charles.girar...@embl.de wrote:
Hi Shane,
We
Hi Yec'han,
Could you check that the 'password' column for the user in question in
the 'galaxy_user' table in the database does not begin with $PBKDF2$?
If not, do you have any debug logs from the FTP session and server
that provide details on the failure?
--nate
On Wed, Mar 5, 2014 at 10:36
Hi Ravi,
Are your datasets stored on a shared filesystem (e.g. NFS)? If yes,
you could try setting `retry_job_output_collection` to something 0
in universe_wsgi.ini? NFS attribute caching can produce behavior like
this.
--nate
On Wed, Mar 5, 2014 at 11:46 AM, Sanka, Ravi rsa...@jcvi.org wrote:
Hi Jennifer,
Thank you for this information. I was able to troubleshoot the bowtie2_indices.
Like Bjoern said the bowtie2 tool needed to be reinstalled because the
tool_table does not load the correct indices.
I am still trying to wrap my head around the different toolsheds.
The main tool shed
Hi fellow galaxy devs,
I am trying to understand how to implement the galaxy database and get an idea
of how big it could get. Currently we are running galaxy on a webserver, and
want to have the postgresql db on locally mounted partition and not on an NFS
partition. This limits us to around
Is there a way to have conditionals and loops for the various steps in a Galaxy
workflow?
For example, a conditional might be used to branch to various steps based on
the previous steps. Also, a step may need to be repeated until it produces a
particular output.
Here is an actual use case:
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