OK data library, (brand new). I upload one BAM file using galaxy's "Add
Dataset"
I start a new history, titling it, "testing multiple use". I import to
current history. I run a job that reads the BAM file and produces some
output.
Everything works. I have 13 output data sets in the history, al
Hi Galaxy Team,
I am using custom genome build for creating a sam file. When I am trying to use
the SAM to BAM tool inside Sam Tools with option
locally cached I am getting an error like "Unspecified genome build, click the
pencil icon in the history item to set the genome build".
I added the cu
I have a long string of steps dying on the last step because GNUPLOT sends
a warning to the log which galaxy faithfully records 11 faithful times in
my history files. The 10 other files have downloadable content, and in
fact, outside of galaxy the plot works. It is simply changing some
intervals.
Hai Galaxy Team,
I have created a .sam file using my own tool. I used a custom genome that I
added to the bowtie_indices.loc.
I want to create another tool which will contain 3 steps,
1. samtool view (sam to bam conversion)
2. samtool sort (sorting bam file)
3. samtool index (creating .bai file)
On 05/04/2012 04:06 PM, Kleo Achilleos wrote:
Hans, thank you for your reply.
I added the path in run.sh located in galaxy_dist
export PYTHONPATH=/usr/local/devel:$PYTHONPATH
but I still get the same error
/
/
/
"/usr/local/devel/NSISSoft/NSISToolkit/NSISApps/SmplTK/load_compounds.py",
line
Hans, thank you for your reply.
I added the path in run.sh located in galaxy_dist
export PYTHONPATH=/usr/local/devel:$PYTHONPATH
but I still get the same error
*
"/usr/local/devel/NSISSoft/NSISToolkit/NSISApps/SmplTK/load_compounds.py",
line 29, in
from NSISSoft.NSISBase import Messengers
*
*
Hi,
We have been working with a relatively old distribution that does not have the
purge datasets feature in the history menu. We just pulled a new galaxy
distribution, and I was trying to test this feature. I tried many scenarios and
I always get "0 datasets have been deleted permanently" and
Hello,
We have an existing galaxy instance that uses MySQL, has workflows and data
libraries and countless changes to the source code and tools. We would like
to save the database, workflows and data libraries but bring all the
sourcecode up to date with the standard galaxy code. Because over 3000
Hi,
I would like to report about some uploading problem on Galaxy.
When I tried to upload a html file which contains a href link, Galaxy failed
with the following error message:
"The uploaded file contains inappropriate HTML content".
Anyway, I found a post about a similar issue and as a result
Sir,
I would like to use PCA for a set of FASTA formatted 1400 sequences (in a
single file).I have stored all fasta formatted sequences in a text file. If
there is any problem for it, you can help me in doing the corresponding
analysis using R.
I am herewith giving a weblink for R, which uses
Hi everyone,
I have a problem about configuring Proftpd and Mysql with galaxy, i have
followed the steps from the galaxy wiki about ftp. I have created a database
'galaxy' and a user mmonsoor which has all the rights on the database. I think
that the reason is about the proftpd.conf, below is
Thank Nate for your help.
Visualization menu is now effective.
However, I still have the problem of updating eggs. Indeed, galaxy is installed on a virtual machine and jobs run on SGE cluster. But I have been discouraged by my system administrator to run fetch_eggs.py scripts from our cluster no
On 05/03/2012 08:29 PM, Robert Chase wrote:
Hello,
We have an existing galaxy instance that uses MySQL, has workflows and
data libraries and countless changes to the source code and tools. We
would like to save the database, workflows and data libraries but bring
all the sourcecode up to date
Hi Kleo
The easiest way is to add the path information to 'run.sh', eg:
export PYTHONPATH=/data/foo/bar/python2.6/site-packages:$PYTHONPATH
(of course, you need to use a different path)
Regards, Hans
On 05/03/2012 08:29 PM, Kleo Achilleos wrote:
Dear all,
I have a local installation of Gala
14 matches
Mail list logo
