Dear developers,
1. I recently installed galaxy locally. now i am trying to run bowtie2. In
reference genome section the genome is not listed.
2. Is there any way yo secure our data without using the Proxy(nginx).
I Appericiate your suggestions.
Thanks
Sridhar
hello,
I am installing galaxy locally.
I tried to upload a .bam file and I got this message:
Traceback (most recent call last):
File /home/user/galaxy_project/tools/data_source/upload.py, line
386, in module
__main__()
File /home/user/galaxy_project/tools/data_source/upload.py, line
Hi, Merav.
A fully functional Galaxy server relies on a lot of third party software
and the error message you see is probably because you do not have samtools
available - the upload process needs it to make an index for your bam file.
So the solution may be to install the samtools package - eg for
Has the script created multiple histories? That's the intent, that each
file+workflow execution has a separate history.
And, for why that file vanished resulting in the exception -- is it
possible you ran a second instance of the script or moved the file?
-Dannon
On Wed, May 29, 2013 at 1:07
Hi,
If I have some programs in php which I need to integrate in Galaxy as a tool,
can I do it? I know if I have some programs written in Perl, python,java,C or
C++, I can easily integrate them. Can I do the same with a php script?
Regards,
Prasun Dutta
MSc (Bioinformatics)
School of
As long as you're able to execute your php script from the command line, it
should work fine.
-Dannon
On Wed, May 29, 2013 at 7:25 AM, Prasun Dutta prasundutt...@yahoo.co.inwrote:
Hi,
If I have some programs in php which I need to integrate in Galaxy as a
tool, can I do it? I know if I
Ok, got it. Unfortunately this isn't really possible at this time, at
least not without a lot of hacking and dealing with data staging issues and
delays (in downloading data from S3 to local cluster to work, uploading
results back to galaxy server, etc.).
Galaxy, with the exception of the LWR -
Hi,
Most people using the RNA-Seq toolkit use a combination of
Tophat/Cufflinks/Cuffdiff. A known issue is that cufflinks and cuffdiff use
different normalisation schemes (
http://seqanswers.com/forums/archive/index.php/t-26041.html). Users
overcome this problem by running cufflinks with the
Joachim,
I'm unable to duplicate that error, what revision of Galaxy and the tool
shed code are you running?
The path mentioned in the error message is a temporary working directory
that is created for downloading and processing files needed for a tool
dependency. Had the installation
I noticed that if I touch universe_wsgi.ini from the terminal (update its
timestamp) while Galaxy is running then Galaxy restarts. If this is intended,
would it be possible to add a Reload Galaxy button/option in the Server
section of the Admin page that mimics this feature?
Obviously, you'd
On May 22, 2013, at 11:36 AM, Sarah Maman wrote:
Hi everyone,
Galaxy is set up on our cluster, and so far everything is working just fine.
However, we'd like to change the submission queue from the default to a
specific one.
To do so, we tryed to set on the universe_wsgi.ini file the
Strange. When I just wget that link in a terminal, do 'chmod +X blat'
and ./blat, it just works fine.
Could it be that the permissions need to be set by Galaxy?
Version info of the Tool Shed:
*
[galaxy@galaxy galaxy-dist]$ hg summary
parent:
Hi Neil,
I've attached my class function for uploading multiple files.
def upload_files(self, fullpaths):
Uploads files from a disk location to a Galaxy library
Accepts an array of full path filenames
Example: fullpaths = ['/home/username/file1.txt',
The problem is most likely in
~/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py, line 100.
1. current_dir = os.path.abspath( os.path.join( work_dir, dir ) )
2. while dir is set a couple of lines before as: dir = workdir (line
78). workdir is the temporary directory.
3.
Hi, galaxy community:
I’ve set up a local galaxy for our institute, one thing that our users kept
complaining is that when dealing with several dozens of datasets, it became
hard to find a certain data.
I’m wondering is there a way to organize data in history? Say, organizing
datasets in
These are options we'd like to add to Cufflinks, and I've created a Trello card
for this enhancement:
https://trello.com/c/U7nceKdj
I want to add that community contributions via patch or pull request are highly
encouraged and are likely to be quicker than waiting for the core team to get
to
When a user creates an account, s/he can create/copy/delete histories and copy
datasets from history to history to organize data. Each history, then, is a
like a library folder.
Best,
J.
On May 29, 2013, at 11:02 AM, 吳正華 wrote:
Hi, galaxy community:
I’ve set up a local galaxy for our
-- Forwarded message --
From: מירב . mer...@gmail.com
Date: Wed, May 29, 2013 at 8:40 PM
Subject: Re: [galaxy-dev] installing galaxy
To: Ross ross.laza...@gmail.com
It worked!! Thank you very mach [?]
Merav
2013/5/29 Ross ross.laza...@gmail.com
Hi, Merav.
A fully functional
Hello,
I am trying to come up with a number for our local galaxy storage
requirements when we go live (This is an installation for research at
our university).
I checked out the survey that was done a while back for the
GalaxyAdmins. It seems that the bigger installations have allocated
It worked!! Thank you very mach
Merav
2013/5/29 Ross ross.laza...@gmail.com
Hi, Merav.
A fully functional Galaxy server relies on a lot of third party software
and the error message you see is probably because you do not have samtools
available - the upload process needs it to make an
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