On 06/09/2014 07:33 PM, Malcolm Tobias wrote:
All,
I apologize for an off-topic question, by my update failed:
[galaxy@login002 galaxy-dist]$ /export/mercurial-1.7.5/bin/hg pull -u |
tee hg.pull.out
...
added 3716 changesets with 9929 changes to 2124 files (+46 heads)
...
merging
Hi,
I am trying to install the tool htseq-count from the tool-shed. I had a
problem in the first installation so I uninstalled the tool and all its
dependencies (numpy, samtools 0.1.19 and pysam) from the 'manage installed
tool shed repositories) and installed it again but then I get installation
Hi Karen,
Sorry your having trouble with installing the tool. It seems that the somehow,
the numpy dependency didn't install properly or isn't being found during the
HTSeq install. Is there any other info in the log to indicate an issue with
installing Numpy? Also, what OS are you running
When trying SAM/BAM to Counts I get the following error message: pysam
not installed; please install it
But a) pysam was not in this tool dependencies;
b) pysam/0.7.7 is already installe
--
[image: Israel Bravo on about.me]
Israel Bravo
about.me/bravobih
http://about.me/bravobih
I installed a local instance of galaxy approximately a month ago (build
2014.04.14).
I was having an issue with the Data Manager to fetch reference genomes and
after checking to see if there was a newer version of galaxy, I decided to
update and see if that fixed my problem.
I ran hg pull and
Hey Stephen,
Can you look in the server logs to see if there are any errors being
reported? Or if there are any javascript errors in the browser window?
You may also want to try clearing your browser cache.
-Dannon
On Tue, Jun 10, 2014 at 1:54 AM, Stephen E sedwards...@hotmail.com wrote:
I
Hello All,
Thanks for the well laid out e-mails and great discussion. I think
John-Paul's comment about the code growing up organically is probably
exactly right. (A link below has some details from Nate about this).
So late last night I opened a sprawling pull request that cleaned up
a lot
Is there a way to look at how long a galaxy tool takes to run?
Jim
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Is there any way to access a list of repository updates in a toolshed,
perhaps as an RSS feed? Alternatively, is this data available internally
and it just requires writing a route to handle that query?
As of now when I log into my toolshed I'm faced with a page of
meaningless hashes and version
Hi Everyone,
This is follow-up information/questions to the issue I ran into with the galaxy
June 2nd, 2014 update. I hope to receive feedback on how to proceed.
Background:
- Running Galaxy (DB Schema 118) with a MySQL 5.5 back-end
- When updating galaxy to the june 2nd
Hello,
This is largely a repost from the biostar forum following the suggestion
there to post here.
I'm doing my first steps in setting up a Galaxy server with an LSF job
scheduler. Recently LSF started supporting DRMAA again so I decided to give
it a go.
I have two setups. The one that works is
This is just a guess, which may help you troubleshoot.
It could be a that python is reaching a stack limit: run ulimit -s and set it
to a higher value if required
I’m completely guessing here but is it possible that the DRMAA is missing a
linked library on the redhat system – check with ldd?
Thanks for proposing a patch.
We're looking at trying it out on our code base but are at least a few
revisions behind and may need to do a little back porting (or catching up).
Let me make sure I understand the intention of the patch, though.
From the code changes, I trust that the intention
On Tue, Jun 10, 2014 at 1:50 PM, John-Paul Robinson j...@uab.edu wrote:
Thanks for proposing a patch.
We're looking at trying it out on our code base but are at least a few
revisions behind and may need to do a little back porting (or catching up).
I think it has been a while since this stuff
Hi all,
I'm working with a problem with user uploaded files. After digging through the
logs a bit and running the commands on at a time manually I think I've narrowed
it to a permissions problem. This was confirmed by just running galaxy as root
and the problem went away ;)
-bash-4.1$
You didn't include this context, but I am guessing you are attempting
to run jobs as the real user? If not, ignore the rest of the e-mail.
I would generally not recommend running the uploads as real user -
it is a complex process but should go relatively quick.
Understand that may not be
Hi Jon and thanks for the reply.I am attempting to run jobs as the real
user as jobs will go to our HPC cluster. This will be an enterprise server.
/panfs/storage.local/scratch/galaxy-data/ is world writable-
drwxrwxrwx 4 galaxy galaxy 4096 May 7 09:08 galaxy-data
as is tmp
Hi Greg,
When I trying to upload a next release version o my
https://toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf converter
program to Community Toolshed, I am getting an internal error message.
I am uploading a tar.gz file to the page https://toolshed.g2.bx.psu.edu/
but this fails.
Could
On Tue, Jun 10, 2014 at 7:37 AM, Karthik Gururaj gururaj.kart...@gmail.com
wrote:
Thanks - will take a look at the Tool Shed and see if there is anything
there we can use in safe manner. Else, the old fashioned way of asking
users to test out on their tools on a standalone Galaxy system and
Sorry, I meant Tool Factory when I wrote Tool Shed in my previous email.
On Tue, Jun 10, 2014 at 5:25 PM, Ross ross.laza...@gmail.com wrote:
On Tue, Jun 10, 2014 at 7:37 AM, Karthik Gururaj
gururaj.kart...@gmail.com wrote:
Thanks - will take a look at the Tool Shed and see if there is
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