Hi
You do not specify which proxy server it is, for example MS TMG ( CNTLM
auth ) / Squid. For CNTLM based authentication you could make use of the
CNTLM application in most repositories to run a local proxy instance and
configure your galaxy user environment with
Peter, Björn,
The August Galaxy release is out, and the template_command is now in the
stable repository and branch. Regarding matplotlib and numpy, I
currently only see matplotlib depending on the 74c21f9bdc39 revision of
numpy. Is this still an issue, or has it been resolved?
--Dave B.
On Tue, Aug 13, 2013 at 2:01 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter, Björn,
The August Galaxy release is out, and the template_command is now in the
stable repository and branch. Regarding matplotlib and numpy, I currently
only see matplotlib depending on the 74c21f9bdc39 revision of
Hey All,
Apologies for all the questions on the mailing list...I am having a lot of
difficulty getting our local Galaxy working.
Currently I have galaxy running but when I try run a job it just stays on
Job is waiting to run and never runs.
I have read the guide and wiki but can't seem to solve
I am totally lost on what is happening now, I have Galaxy running but jobs
are not being run:
This is my setup:
torque:
qmgr -c 'p s'
#
# Create queues and set their attributes.
#
#
# Create and define queue batch
#
create queue batch
set queue batch queue_type = Execution
set queue batch
I think you are experiencing this bug, which is a major problem with the latest
AMI.
https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-to-mnt
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of
Hi Galaxy Tool developers!
I have started to integrate the HOMER suite into Galaxy. My initial
attempt can be found here:
https://github.com/bgruening/galaxytools/tree/master/homer
Currently, we make use of:
- Tool Shed definitions of all required 3rd Party Software
- datatype definitions
-
Hi Dave,
for us I think everything is fixed. But we had a bad bug in the 'single
revision' implementation of the new 'Tool dependency definition' type.
We had something like that:
A (tool dependency definition) - B (tool) - C (workflow)
We changed A (that was numpy) and thought it would be ok
Thank you for the reply.
I do not have any working knowledge of ubuntu and linux commands.
Moreover, I work from a windows computer.
I can see that this problem is being discussed since July12th
http://dev.list.galaxyproject.org/Cloudman-Software-does-not-work-due-to-broken-symlinks-td4660619.html
Hello,
I am trying to use the ENA galaxy import feature. This involves going to
the analyze menu in galaxy and clicking the link 'EBI SRA'
which is encoded as
http://www.ebi.ac.uk/ena/data/search?GALAXY_URL=https%3A//main.g2.bx.psu.edu/tool_runner%3Ftool_id%3Debi_sra_main
This does not seem
Dear sir,
please add reference genome of Zebra finch genome in Bowtie2 and Tophat2
option in galaxy. thank u
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Dear all,
I have managed to use something like
outputs
data format=fasta name=output label=#echo os.path.splitext (str
($input.name))[0]#-ORF.fasta/
/outputs to display the wanted label for the dataset in the history.
However when I applied the same code to other tool
Hi Vijay,
For right now, using a Custom reference genome with these tools is the
best solution:
http://wiki.galaxyproject.org/Support#Custom_reference_genome
This genome in Galaxy is sourced from UCSC, as you probably know:
http://wiki.galaxyproject.org/Support#Reference_genomes
The
Hi Tin,
I am going to move this over to the galaxy-...@bx.psu.edu mailing list
(good for local install questions) to give it better viability.
I am by no means the best person to help with this, so hopefully others
will jump in, but just from looking at this I am wondering if you
shouldn't
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