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
__main__()
File "/home/user/galaxy_project/tools/data_source/upload.py", line
375
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
Hi all,
I am building a wrapper around BLAT, and have put it locally in a
toolshed. However, the automatic installation of dependencies fails:
*
Tool dependency installation error:
[Errno 2] No such file or directory:
'/home/galaxy/galaxy-dist/database/tmp/tmp2J7K_L/da
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 A
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 Biologica
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 wrote:
> 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 writte
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 -
h
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 follo
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 succee
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,
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 th
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: 9320:47ddf167c
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
On Wed, May 29, 2013 at 2:54 AM, sridhar srinivasan
wrote:
>
> Dear developers,
>
> 1. I recently installed galaxy locally. now i am trying to run bowtie2. In
> reference genome section the genome is not listed.
>
For 1 you might want to take a look at:
http://wiki.galaxyproject.org/Admin/NGS%20L
Hi guys,
we are currently estalishing our own local Galaxy instance. However, when we
try to install "Repository 'ncbi_blast_plus'" from the Galaxy main tool shed
via the admin pages, we obtain the following error
"Internal Server Error
Galaxy was unable to sucessfully complete your request
A
On May 24, 2013, at 7:27 AM, Marc DELOGER wrote:
> Hello,
>
> I tried to download several times the several egg on these following mirrors
> but the download is always blocked near 50%...I asked several different
> people and they all have the same problem :
>
> http://eggs.g2.bx.psu.edu/mercu
On Wed, May 29, 2013 at 8:33 AM, Keilwagen, Jens
wrote:
> Hi guys,
>
> we are currently estalishing our own local Galaxy instance. However, when we
> try to install "Repository 'ncbi_blast_plus'" from the Galaxy main tool shed
> via
> the admin pages, we obtain the following error
>
> "Internal S
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. cu
Hello Jens,
What does your Galaxy paster log show that is related to the internal server
error?
Greg Von Kuster
On May 29, 2013, at 10:13 AM, Peter Cock wrote:
> On Wed, May 29, 2013 at 8:33 AM, Keilwagen, Jens
> wrote:
>> Hi guys,
>>
>> we are currently estalishing our own local Galaxy inst
Joachim,
I believe the behavior you're experiencing may be due to an issue that
was fixed between 9320:47ddf167c9f1 and the current stable branch. I
would recommend updating to the most recent stable branch of
galaxy-central.
--Dave B.
On 5/29/13 09:30:37.000, Joachim Jacob | VIB | wrote
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 fo
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 t
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 i
-- Forwarded message --
From: מירב .
Date: Wed, May 29, 2013 at 8:40 PM
Subject: Re: [galaxy-dev] installing galaxy
To: Ross
It worked!! Thank you very mach [?]
Merav
2013/5/29 Ross
> Hi, Merav.
> A fully functional Galaxy server relies on a lot of third party software
> an
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
abo
It worked!! Thank you very mach
Merav
2013/5/29 Ross
> 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
Raj,
maybe others have a different view on this but I think just throwing you a
number is quite useless.
It all depends on YOUR data storage strategy/policy.
How long can researchers store/use their data. What are their maxed quota...Is
it backuped elsewhere, how many users. Is it public wha
Andreas,
export your history to tgz.
then locally import it.
I have to say that we do this for backup purposesbut it is a
pain.exporting takes sometimes ages even for small histories.
I am not sure how well synced your databases and such should be.(unique
identifiers and such).
Hi John,
Can you please have a look at Neil's question.
Thank you,
-Alex
From: Burdett, Neil (ICT Centre, Herston - RBWH)
Sent: Thursday, 30 May 2013 4:30 PM
To: Khassapov, Alex (CSIRO IM&T, Clayton)
Subject: Multi File upload api
Hi Alex,
The file "galaxy-dist/scripts/api/example_wa
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