Mic;
> I have tried to install gff with easy_install, but I got the following
> error:
> $ easy_install --prefix=/home/mic/apps/pymodules -UZ
> https://github.com/chapmanb/bcbb/tree/master/gff
> Downloading https://github.com/chapmanb/bcbb/tree/master/gff
> error: Unexpected HTML page found at
Hello to All,
I would like to reiterate this problem because it is causing major
problems in tha managment of our Galaxy instance
Are there some clues on how to solve this issue ?
Best regards,
--
Olivia Doppelt-Azeroual, PhD
Pasteur Institute, Paris
Le 23/04/13 22:38, Fabien Mareuil a écr
Olivia,
There's a fix for this available in galaxy-central, but I'm surprised
you're seeing it in -dist as I thought the problem was introduced after the
dist freeze. Can you provide the output of 'hg tip'?
-Dannon
On Mon, Apr 29, 2013 at 6:53 AM, Olivia Doppelt
wrote:
> Hello to All,
>
> I w
Hey Rob,
That example_watch_folder.py does just submit exactly one at a time,
executes the workflow, and then does the next all in separate transactions.
If you wanted to upload multiple filepaths at once, you'd just append more
to the ''filesystem_paths' field (newline separated paths).
-Dannon
Hello Peter,
Thanks for your email - It's been on my list for a while to revisit this, so
your request is timely. I've added the following Trello card for it.
https://trello.com/card/toolshed-enhancements-to-page-flow/506338ce32ae458f6d15e4b3/813
Greg Von Kuster
On Apr 25, 2013, at 5:13 AM, P
Hey, it is not just me! Your commits are definitely in galaxy-dist,
they just might not be part of the most recent stable tag.
https://bitbucket.org/galaxy/galaxy-dist/commits/80291f7ad4576c95f70eaed2f36cc5a95cf303fb
The hg new workflow is easy to mess up, it use to be that you could
just trust w
Dear Dannon,
Here is the 'hg tip' result:
changeset: 9312:788cd3d06541
tag: tip
parent: 9310:19f6e62bd372
parent: 9311:d7f37a2fe690
user:Nate Coraor
date:Mon Apr 08 12:30:08 2013 -0400
summary: Merged stable.
--
Olivia
Le 29/04/13 15:05, Dannon Baker
Hi Dannon,
Thanks for the response. Sorry to be pedantic, but just to make sure that I
understand the interpretation of this field on the other side of the API, I
would need to have something like the following:
data['filesystem_paths'] = "/home/me/file1.vcf \n /home/me/file2.vcf /n
/home/me/file
Hi Jean-Francois,
Were you able to update to the next galaxy-dist and test? This issue
should be resolved in 8771:ae446180fd11, which was added just after the
distribution you were using previously.
-Dannon
___
Please keep all replies on th
Hi Peter,
>How did you install them? Via the automated Tool Shed install,
>or manually?
I installed the tool wrappers via the Tool Shed, and Blast 2.2.28 is already
installed on my cluster so I put the path in my environment setup file.
>How did you setup the databases?
I added the existing data
On Mon, Apr 29, 2013 at 2:53 PM, Ganote, Carrie L wrote:
>
> Hi Peter,
>
> >How did you install them? Via the automated Tool Shed install,
> >or manually?
>
> I installed the tool wrappers via the Tool Shed, and Blast 2.2.28 is
> already installed on my cluster so I put the path in my environment
On Wed, Apr 24, 2013 at 10:14 PM, Peter Cock wrote:
> On Wednesday, April 24, 2013, Dave Bouvier wrote:
>> I've updated the relevant trello card, my plan is to focus on
>> improving the testing framework over the next few days.
>>
>>--Dave B.
>
>
> Great - Thanks guys,
>
> Peter
Hi Dave,
Wha
Hi Peter,
>I'm not 100% sure but I think the BLAST 2.2.26+ which Galaxy installed
>via the Tool Shed will take priority over the system installed BLAST 2.2.28+
>already on the cluster.
Blast 2.2.26 probably would take priority, if I installed it =D but I didn't
set up the missing tool dependenc
On Mon, Apr 29, 2013 at 3:38 PM, Ganote, Carrie L wrote:
> Hi Peter,
>
>>I'm not 100% sure but I think the BLAST 2.2.26+ which Galaxy installed
>>via the Tool Shed will take priority over the system installed BLAST 2.2.28+
>>already on the cluster.
>
> Blast 2.2.26 probably would take priority, i
You can verify this with 'hg branch', but it looks like you're tracking the
default branch of -dist, where you want to be on stable. 'hg update
stable' should fix this, and the issue you're seeing.
You should only have to do this once, next time you update (with just hg
pull -u) you'll stay on st
Yep, that example filesystem_paths you suggest should work fine. The
sleep() bit was a complete hack from the start, for simplicity in
demonstrating a very basic pipeline, but what you probably want to do for a
real implementation is query the dataset in question via the API, verify
that the datat
Hello Yongde,
The list of genomes is gathered from many sources and is
comprehensive to facilitate external display functionality (at UCSC
- main and microbial-, Ensembl, Wormbase, etc.). When assigning a
dataset in a standard format to one of these sources, those
Hi Dannon,
I've written some code to (i) query a dataset to ensure that it's been
uploaded after a submit and (ii) to ensure a resulting dataset has been
written to the file.
*#Block until all datasets have been uploaded*
libset = submit(api_key, api_url + "libraries/%s/contents" % library_id,
da
I ran into the same problem as Peter, and you're post was very helpful
John. Thanks for the workaround!
Lance
Peter Cock wrote:
On Thu, Apr 11, 2013 at 5:02 PM, John Chilton wrote:
Hey Peter,
Hopefully Nate will have some wisdom, all I have is a workaround (I
have fought with this on mu
Dear Galaxy Team,
I'm using the psu public galaxy software and cannot get my workflows to use
the input files I'm selecting. Everytime I try to run the workflow, I enter
all of the input files that I want to use, but after I hit run, the
operations are performed only using my most recent Galaxy fi
Hi Amanda,
Sorry about the inconvenience. There's a fix for this issue in
galaxy-central that will be available the next time main.g2.bx.psu.edu is
updated. Until then, if you remove the "input dataset" step from your
workflow and allow the tool itself to act as the starting point, it should
all
Correction. The above were not reliable methods to ensure the file was
copied into the data library. Checking for file_size != 0 was also not
effective for large files.
Dannon, can you tell me which field we should query and what state/message
which will allow us to avoid race conditions?
The onl
Hi,
I'm trying to use the tool, however, when I run it I get:
python create_galaxy_users.py
Traceback (most recent call last):
File "create_galaxy_users.py", line 2, in
from scripts.db_shell import *
ImportError: No module named scripts.db_shell
I've set my PYTHONPATH to be ~/galaxy
Neil,
AFAIK, python will not load a module unless the relevant script file is
marked as executable by the current user?
Try something like:
chmod ugo+x scripts/db_shell.py
and see if that fixes your problem?
On Tue, Apr 30, 2013 at 11:50 AM, wrote:
> Hi,
> I'm trying to use the tool, howev
Thanks for the info Ross
But I still get the same error
"ImportError: No module named scripts.db_shell"
After chmod 777 scripts/db_shell.py
When you get "ImportError: No module named galaxy" for example it's because
the PYTHONPATH isn't set so I guess there's some variable I need to set for t
Funny, it works for me.
One last thought: You do still have the distributed __init__.py readable by
your userid in /scripts so the module loader knows it's a python package
directory?
On Tue, Apr 30, 2013 at 12:05 PM, wrote:
> Thanks for the info Ross
>
> ** **
>
> But I still get the sam
Thanks Ross. I was missing __init__.py
It now works thanks
Neil
From: Ross [mailto:ross.laza...@gmail.com]
Sent: Tuesday, 30 April 2013 12:14 PM
To: Burdett, Neil (ICT Centre, Herston - RBWH)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Command Line Tool for Creating New Users
Funn
This follows on from Kenneth Auerbach's question Sep 12, 2012: Galaxy error
running NCBI BLAST: blastx
http://dev.list.galaxyproject.org/Galaxy-error-running-NCBI-BLAST-blastx-td4656210.html
I wish to use a local copy of the genbank database for searches. The
genbank db files are sitting in a fold
Thank you it is working.
On Mon, Apr 29, 2013 at 8:34 PM, Brad Chapman wrote:
>
> Mic;
>
> > I have tried to install gff with easy_install, but I got the following
> > error:
> > $ easy_install --prefix=/home/mic/apps/pymodules -UZ
> > https://github.com/chapmanb/bcbb/tree/master/gff
> > Downlo
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