Hi
Are you looking for any special GEO data, which is not mirrored at the
ENA? If not, you can probaly use the "Get Data" -> "EBI SRA" tool,
which is part of the installation.
Also, have you looked at the toolshed? e.g.
https://toolshed.g2.bx.psu.edu/view/matt-shirley/ncbi_sra_toolkit
Rega
Hello,
I am trying to use parallelism in Galaxy. I added this entry to the tool
xml config:
for each sequence in a file
But when I run the job, the log shows the next:
Traceback (most recent call last):
File "/home/ralonso/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 158,
Hi Roberto
just double checking: are you using a PostgreSQL database, or are you
relying on the built in SQLite?
Hans-Rudolf
On 02/05/2015 02:26 PM, Roberto Alonso CIPF wrote:
Hello,
I am trying to use parallelism in Galaxy. I added this entry to the
tool xml config:
for each sequen
Hello,
I am using the galaxy built-in database, SQLAlchemy on top of sql lite?
May I swith to postgress?
Regards
On 5 February 2015 at 14:41, Hans-Rudolf Hotz wrote:
> Hi Roberto
>
> just double checking: are you using a PostgreSQL database, or are you
> relying on the built in SQLite?
>
> Ha
Hi
I can't promise, this is the solution for your specific problem, but you
will always run into "database is locked" issue, when using SQLite.
Hence, I strongly recommend to switch to a PostgreSQL database as the
back-end for Galaxy (see also:
https://wiki.galaxyproject.org/Admin/Config/Per
Hi Roberto, Hans-Rudolf,
I can confirm from personal testing that enabling the
parallelism task-splitting in Galaxy does not work
well with SQLite.
This caused me problems with development and
testing since my development Galaxy instance uses
SQLite. As you found, testing with smaller splits
is o
Hi Stephen,
On Wed, Feb 4, 2015 at 8:30 PM, Stephen Rosen wrote:
> Hi Nate,
>
> Thanks so much for helping me out with this.
>
> It seems that I've miscommunicated what I'm doing a little bit.
> I'm installing a package from that git repo using pip separately from
> running the galaxy setup scri
Hello guys,
So I've been working on the Galaxy report page.
It works fine however I'm using MySQL and I'm getting some server errors on
some webpages.
I found the solution:
https://lists.galaxyproject.org/pipermail/galaxy-dev/2009-August/000641.html
But can some please confirm the following:
Hello,
I am trying to use parallelism in Galaxy. I added this entry to the tool
xml config:
for each sequence in a file
But when I run the job, the log shows the next:
Traceback (most recent call last):
File "/home/ralonso/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 158,
Actually, here's what I came up with :
diff users.py ARCHIVES/users.py_20150205_9.28.18
23c23
< q = sa.select( ( sa.func.date( galaxy.model.User.table.c.create_time
).label( 'date' ),
---
> q = sa.select( ( sa.func.date_trunc( 'month', sa.func.date(
> galaxy.model.User.table.c.cr
Thanks Hans-Rudolf. I didn't see the EBI SRA link before. But not sure
what will do what I want. I want to be able to plug in an SRA # and have
the tool download the data and prep it for analysis. Right now, it looks
like I need to click through the EBI website to get the data. I found a
tool
Hi Edgar
Well, if it works, and you get the right numbers, then it is probably
correct
It is difficult to identify your changes, but I can show you what I have
done in order to get all the options to work with our MySQL database. I
hope I refer to the same lines in 'jobs.py', don't I?
Hi again
for "jobs.py" I have modified the same lines as you,
plus line 285 (group_by)
for "users.py I have modified the same lines as you
Hans-Rudolf
On 02/05/2015 04:20 PM, Fernandez Edgar wrote:
Actually, here’s what I came up with :
diff users.py ARCHIVES/users.py_20
Good catch on that one!
There wasn't originally the date_trunc function there but that groups the jobs
by months together.
Thanks!!!
Cordialement / Regards,
Edgar Fernandez
-Message d'origine-
De : Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Envoyé : February-05-15 10:49 AM
À : Fernandez Edg
Here’s some other modifications I’ve made that should be logged somewhere :
diff workflows.py ARCHIVES/workflows.py_20150205_11.37.57
143c143
< q = sa.select( ( sa.func.date(
model.StoredWorkflow.table.c.create_time ).label( 'date' ),sa.func.count(
model.StoredWorkflow.table.c.id ).l
Hi Martin,
Many thanks for your answer, and sorry for this late reply I've been off sick.
In order to ease my migration, I am looking into reducing the number of tools
installed that are not in used. We do run a cut down version of galaxy with
much fewer tools that currently in Galaxy Main, but
Hi Anne,
as far as I know Galaxy does not have an API endpoint to uninstall
repositories. I would use an admin interface for this - the process of
uninstalling is pretty fast and unless you have some crazy number of
installed tools it should be done quick.
M.
On Thu Feb 05 2015 at 12:24:03 PM An
Hi Roberto,
It looks like you are probably still using the default sqlite database. You’ll
want to update to using e.g. postgres when exploring these more database
intensive functions. See e.g.:
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Switching_to_a_database_ser
Hey Guys,
Thanks for the patches - it looks like Eric Enns came up with similar
ones a while back (
http://dev.list.galaxyproject.org/Patch-in-reference-to-trello-card-968-td4660438.html).
The bad news is I just went through and made a bunch PEP-8 fixes to the
reports code so all the patches are
Assuming grid engine is working outside of Galaxy and the Galaxy user
can say qsub files just fine - then you need to install the sun grid
engine libdrmaa package - or build from scratch. Assuming you have
done that and the resulting .so file is
/usr/lib/gridengine-drmaa/lib/libdrmaa.so. Then all y
I believe we updated usegalaxy.org and Bjoern Docker galaxy images to
the latest Galaxy release - both which leverage this feature and
didn't encounter issues with either. Is it possible you updated nginx
as part of the release as well? At least in the past the upload
feature has had problems with
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