Hi Josh
Are you running the additional reports web site?
see: 'run_reports.sh' and 'reports_wsgi.ini'
We use this extra web site a lot for debugging. It helps tracking what
an individual user is doing - kind of 'big brother is watching you'
Regards, Hans
On 04/24/2012 10:51 PM, Dannon
Hi Deepthi
Have a look at:
http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20
section: 'Variable Static Outputs determined by parameter values'
Regards, Hans
On 04/24/2012 09:29 PM, Unknown wrote:
Hi all,
Can I implement a tool which run 2 different algorithms and providing
Hi Dan
There seems to be several issues connected with each other or not, I
don't know.
- Let's start with the 'curiosity': Do you get this problem with any
tool? Does it also happen with a 'simple' (ie not using R) tool you
add?
- When you execute your R script on the command
Hi Sarah,
You should be able to do this with the -r option of the clone command, so: `hg
clone -r b258de1e6cea https://bitbucket.org/galaxy/galaxy-dist`.
-Dannon
On Apr 25, 2012, at 3:08 AM, Sarah Maman wrote:
Hello,
I would like to get source code with Mercurial of this tarballs :
Hi Leandro
brilliant! - adding the line manually did indeed fix the problem and I
could remove the re-activate line 36 and 37 in ~/lib/galaxy/app.py
Thank you very much!
now have to find out why this line was not inserted in the first place
Hans
On 04/24/2012 06:04 PM,
Hi,
Thanks a lot it actually helped. It is not exactly as straightforward in
drmaa.py but somehow I could manage.
However, it was not the problem. For some reason, the user needs to
write files from the node to job_working_directory/00X// and the
latter is not world-writable. I had to
Excuses for the repost, but I still hope somebody can answer this question?
Is it possible to pass the parameters of an input dataset? For example:
the user selects a dataset of the history. I want to pass to my
wrapperscript the input parameters of that dataset (the information you
see when
Thank you very much Dannon, it works.
The more I discover Galaxy, the more I appreciate its use. Again, thank
Galaxy team for this great tool.
Sarah Maman
Dannon Baker a écrit :
Hi Sarah,
You should be able to do this with the -r option of the clone command, so: `hg
clone -r b258de1e6cea
Hi everyone,
I'm (still) having issues with running jobs as the real user on our PBS
Pro cluster. When I try running a job, it ends up in error state and
displays the following error message:
touch: cannot touch `/home/galaxy/.drmaa/9167860.pbs-master2.embl.de.started':
Permission denied
Hi everyone,
I just wanted to ask how the extra_file_path is handled in case of job
running as the real user since the file_path is only writable by the
galaxy user. Any clue?
Thanks,
L-A
___
Please keep all replies on the list by using
Thanks Hans.
On 4/25/12, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Deepthi
Have a look at:
http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20
section: 'Variable Static Outputs determined by parameter values'
Regards, Hans
On 04/24/2012 09:29 PM, Unknown wrote:
Hi all,
Can
Hello Hans-Rudolph,
On Wed, Apr 25, 2012 at 1:37 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Dan
There seems to be several issues connected with each other or not, I don't
know.
- Let's start with the 'curiosity': Do you get this problem with any
tool?
No. And, I should be a bit
I was running a single instance of galaxy on my own machine, playing with
library_import and figuring why BAM files were getting errors on upload.
(It is a path matter, when one drops into the subshell and the workaround
is
ln -s /usr/bin/samtools /home/galaxy/bin/samtools
)
Anyway, I seemed to
Hi Galaxy-Dev,
I have a a special set of .txt files which contains some comments and tabular
feilds.
I want to make them as a different group so that I can list them without any
other .txt files.
I went through the Add New Data Type section.But I didnt get a clear idea of
how to do it?
The
On Wed, Apr 25, 2012 at 12:56 PM, Michael Moore
michaelglennmo...@gmail.com wrote:
My registration was gone. My admin_user was overwritten. I re-registered,
and restored the file settings and restarted galaxy, but now no login
sticks. It does not complain about a registered user, but it does
On Wed, Apr 25, 2012 at 9:53 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hello Hans-Rudolph,
On Wed, Apr 25, 2012 at 1:37 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Dan
There seems to be several issues connected with each other or not, I don't
know.
- Let's start with the
On Wed, Apr 25, 2012 at 11:48 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Wed, Apr 25, 2012 at 9:53 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
Hello Hans-Rudolph,
On Wed, Apr 25, 2012 at 1:37 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Dan
There seems to be several issues connected with
Hi all,
I went through the example given in the Adding New data type section.
Generally what should be the contents of the
galaxy.datatypes.new_datatype.py file?
Thanks,
Deepthi
On 4/25/12, Unknown deepthither...@gmail.com wrote:
Hi Galaxy-Dev,
I have a a special set of .txt files which
Hello,
I'd am trying to export histories to upload to another galaxy instance.
For some histories, it works fine. However, for others, I get an
error. When I turn on debug, I get the error pasted below. Any
thoughts on what is the cause of object has no attribute 'hid'?
Thanks!
Hi all,
This is what I did:
$output = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[0] *
21*`;
The STDOUT was captured and redirected after I added the 21. Now, the
result of the operation isn't in red.
On Wed, Apr 25, 2012 at 8:44 AM, Ciara Ledero lede...@gmail.com wrote:
To
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