On Wed, Aug 7, 2013 at 3:33 PM, Ganote, Carrie L wrote:
> Hi John,
>
> That was it. I feel silly. I still have a lot of tooth-cutting to do on
> python!
>
> I saw the parallel tags in the Blast tool and was very intrigued, but
> couldn't find reference to it in the read-the-docs or on the Galaxy
Yes,and I also have the same confuse about that.Actually when I set server:
in the universe_wsgi.ini as follows for a try,my Galaxy doesn't work with
Cluster,if I remove server:,it work .
[server:node01]
use = egg:Paste#http
port = 8080
host = 0.0.0.0
use_threadpool = true
threadpool_workers = 5
A new tools volume will be released shortly. For now, you can launch the
previous cloudman release using the following:
https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3&bucket_default=gxy-workshop
On Wed, Aug 7, 2013 at 7:42 PM, Ulyanov_Anatoly <
ulyanov_anat...@allergan.com> wrote:
> H
Hello,
Does anybody use the last Galaxy image? I am running Galaxy image on EC2:
Instance ID i-1b2d3773
Image ID (AMI) ami-118bfc78
It looks as those three tools have configuration problems:
EBOSS
Blast+
meme
For all three I am getting a message that looks like that:
/mnt/galaxy/tmp/
Hi John,
That was it. I feel silly. I still have a lot of tooth-cutting to do on python!
I saw the parallel tags in the Blast tool and was very intrigued, but couldn't
find reference to it in the read-the-docs or on the Galaxy wiki. Perhaps there
is some documentation of this that I missed?
In
I am not sure why the quotations marks are there in the first place,
but I do see the problem. replace and strip return new strings, they
don't modify the existing variable. This is demonstrated below:
% python
>>> x = ' "Moo Cow" '
>>> x
' "Moo Cow" '
>>> x.replace("\"", "").strip()
'Moo Cow'
>>>
Hi List,
I've run into a frustration recently with passing values to the dynamic job
runner from a tool. Here's what's going on:
in ncbi_blastn_wrapper.xml:
...
in dynamic_runner.py:
...
def blastn_wrapper(job):
incoming = dict( [ ( p.name, p.value ) for p in job.parameters ] )
modul
On Wed, Aug 7, 2013 at 5:35 PM, Peter Cock wrote:
> On Wed, Aug 7, 2013 at 5:11 PM, Bjoern Gruening
> wrote:
>> Hi Peter,
>>
>>> Now, back in ncbi_blast_plus, I have revised the
>>> repository_dependencies.xml to declare this new
>>> repository dependency (the revision tag etc is missing
>>> to m
On Wed, Aug 7, 2013 at 5:11 PM, Bjoern Gruening
wrote:
> Hi Peter,
>
>> Now, back in ncbi_blast_plus, I have revised the
>> repository_dependencies.xml to declare this new
>> repository dependency (the revision tag etc is missing
>> to mean the latest version at upload is used):
>
> Mh, I never tr
Hi Peter,
> On Wed, Aug 7, 2013 at 3:54 PM, Peter Cock wrote:
> > On Wed, Aug 7, 2013 at 3:36 PM, Greg Von Kuster wrote:
> >> Hi Peter,
> >>
> >> On Aug 7, 2013, at 10:26 AM, Peter Cock wrote:
> >>
> >>> Hi Greg et al,
> >>>
> >>> For the NCBI BLAST+ wrappers, Nicola has suggested we split
> >>
On Wed, Aug 7, 2013 at 3:54 PM, Peter Cock wrote:
> On Wed, Aug 7, 2013 at 3:36 PM, Greg Von Kuster wrote:
>> Hi Peter,
>>
>> On Aug 7, 2013, at 10:26 AM, Peter Cock wrote:
>>
>>> Hi Greg et al,
>>>
>>> For the NCBI BLAST+ wrappers, Nicola has suggested we split
>>> out the binaries themselves i
Thanks Bjoern,
My hope is that the current export process will help you with whatever you are
manually migrating. If you export the chemicaltoolbox and all of it's
dependencies, you will have a nice tarball of each repository that you want to
manually upload to the main tool shed. Of course,
Hi Greg,
wonderful will test it locally asap and report any error. The most
urgent packages I will migrate manually for the time being. I promised
it far to long.
Thanks Greg!!!
Bjoern
> Hello Bjoern,
>
>
> I have the export repository ( and optionally all repoository
> dependencies ) feature
Hi Peter,
This is a known issue ( not a Tool Shed issue, but a Galaxy issue ) related to
the Select list that gets automatically populated with the "Select one" option.
You have to actually click the x" on this option to eliminate it. Again, this
feature is inherited from Galaxy, so it's not
Hi Greg, Dave,
While logged into the Test Tool Shed as 'iuc', I just created
a new (empty) repository:
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26
See background discussion on this thread:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/015890.html
As 'iuc', I t
Thanks for the update, Dave!
Was delighted to see that the videos from all the talks (except
lightning talks) are up at:
http://wiki.galaxyproject.org/Events/GCC2013/Program
I wanted to ask though, are there specific reasons for not using a
service like YouTube / Vimeo etc?
That would make
I have added an feature request issue on galaxy-extras to support this.
Earlier this year, Hagai Cohen was exploring the existing Galaxy tools
and it seems like some of them expect dataset files to end with .dat.
So I reworked the multiple file dataset stuff so each of the
individual parts ended t
Il giorno mer, 07/08/2013 alle 16.28 +0200, Bjoern Gruening ha scritto:
> > Also, we may wish to add a dependency on BOOST, e.g.
> > http://testtoolshed.g2.bx.psu.edu/view/iuc/package_boost_1_53
> > once this is on the main Tool Shed.
>
> Ok, time to step up and migrate all the stuff to main.
Th
On Wed, Aug 7, 2013 at 3:36 PM, Greg Von Kuster wrote:
> Hi Peter,
>
> On Aug 7, 2013, at 10:26 AM, Peter Cock wrote:
>
>> Hi Greg et al,
>>
>> For the NCBI BLAST+ wrappers, Nicola has suggested we split
>> out the binaries themselves into a separate Tool Shed package,
>> e.g. package_blast_plus_
Hello Bjoern,
I have the export repository ( and optionally all repoository dependencies )
feature working on the test tool shed. The feature allows you to chose a
specific installable revision (if in the browser, by being on the Manage
repository page for that revision or if using the API by
Hi Peter,
On Aug 7, 2013, at 10:26 AM, Peter Cock wrote:
> Hi Greg et al,
>
> For the NCBI BLAST+ wrappers, Nicola has suggested we split
> out the binaries themselves into a separate Tool Shed package,
> e.g. package_blast_plus_2_2_26 and similar for the later releases.
>
> https://github.com
Hi Peter,
> Hi Greg et al,
>
> For the NCBI BLAST+ wrappers, Nicola has suggested we split
> out the binaries themselves into a separate Tool Shed package,
> e.g. package_blast_plus_2_2_26 and similar for the later releases.
>
> https://github.com/peterjc/galaxy_blast/issues/7
>
> I think this
Hi Greg et al,
For the NCBI BLAST+ wrappers, Nicola has suggested we split
out the binaries themselves into a separate Tool Shed package,
e.g. package_blast_plus_2_2_26 and similar for the later releases.
https://github.com/peterjc/galaxy_blast/issues/7
I think this is a good idea.
I'd like to
Hi there,
I am running my own instance of galaxy (April 2013 version) and I have
problems with saved histories. Sometimes the histories do NOT show up at
all at the right hand side (panel remains white with no error message). I
then have make a clone of the history and then I can use it again. I
h
Hello,
I have a very simple jobrunner script that allows only 1 job to be run as this
galaxy is used for one thing in particular which consumes almost all resources.
To do this I set the following:
This works, but is it possible to create a second worker that is only allowe
Hi,
This is my first Galaxy installation setup so apologies for stupid
questions. I am setting up Galaxy on a Cluster running Torque as the
resource manager. I am working through the documentation but I am unclear
on some things:
Firstly I am unable to find : *start_job_runners *within the
univer
On Wednesday, August 7, 2013, Nikhil Mallela wrote:
> Hi,
>
> I am working on the colorspace data.
> I have one old data (*.csfasta, SOLiD4) & one new (*.xsq, 5500xl).
> I wanted to use tophat and cufflinks pipelines with Galaxy,
> Although tophat can make use of colorspace data, but galaxy seems
Hi,
I am working on the colorspace data.
I have one old data (*.csfasta, SOLiD4) & one new (*.xsq, 5500xl).
I wanted to use tophat and cufflinks pipelines with Galaxy,
Although tophat can make use of colorspace data, but galaxy seems to be
accepting only FASTQ format for most of its tools.
And the
Hello Galaxy Team,
I get this error
> "Error reading bam file. This usually indicates a problem with the index
> (bai) file. ArrayIndexOutofBoundsException: 6921 (6921)."
when I finish my pipeline and try do view any of the sam or bam files.
-occurs on both hg19 and hg_g1k_v37
-i tried to sort
Hi Rodolfo,
> On Tue, Aug 6, 2013 at 11:41 AM, Peter Cock wrote:
> > On Tue, Aug 6, 2013 at 5:30 PM, Rodolfo Aramayo wrote:
> >> Dave,
> >>
> >> It did contain errors as reported by tailing the last part of the
> >> INSTALLATION.log
> >>
> >> Thanks
> >>
> >> --Rodolfo
> >
> > Looks like your BO
Hi Peter,
I have used UGene before: it is a nice tool. I am not sure I have
understood your question. The easiest way to integrate your tool in
Galaxy, is that your tool can be driven by the command line (no GUI).
The tool and parameters should be configured by a tool config file, as
you men
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