Hi,
Just checking before I plunge in and upgrade various things. Is the latest
Galaxy and Cloudman ( http://wiki.g2.bx.psu.edu/News/NewCloudManRelease )
ok on Python 2.7.3 ?
And can I ask what Python rev is incorporated in the new Cloudman AMI ?
Presumably a little earlier than 2.7.3. My current
Update : Now my tool creates a html composite output, made of 2 outputs .xxx
and .yyy.
I've added the def get_mime(self) function in the python file describing all
my formats, and now it works.
When I run my tool and click on the eye symbol, I can see a html page with
links to download the
Hi Marine,
Other people may have better ideas, but the way I've always done it is to
ensure that the tool knows how to find the input files inside the
extra_files_path because that's easy to pass.
If $i is the name of data parameter = composite file chosen from the user
history (ie a data input
Hello all,
I'm wondering if it is sensible to make Galaxy tools automatically use
the environment variable $NSLOTS to automatically adjust their
number of threads?
Using $NSLOTS works on SGE, but is it generally used on other clusters?
The idea here is rather than hard coding the number of
You mean the javascript works right? Or did you manage to get the PHP inside?
Alex
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Smithies, Russell
Verzonden: donderdag 14 juni 2012 1:45
Aan: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev]
Hi Greg,
I guess something went wrong while update, because I updated to the
latest changeset:
hg tip | grep changeset
changeset: 7262:4fbd05095ca7
Can it be because I the last time I updated was at least half a year ago
and the toolshed integration has been implemented afterwards? So that
Hi Matthias,
There is really nothing to configure in your Galaxy environment in order to use
the public Galaxy tool sheds. Ideally, you should set the following
configuration setting, but not setting it defaults to using the file named
shed_tool_conf.xml for installed tools anyway.
On Fri, Jun 15, 2012 at 12:17 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hello all,
I'm wondering if it is sensible to make Galaxy tools automatically use
the environment variable $NSLOTS to automatically adjust their
number of threads?
Using $NSLOTS works on SGE, but is it generally
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Hi Greg,
Here is the output of the commands:
hg status
M run.sh
M static/fastx_icons/barcode_splitter_output_example.png
M static/fastx_icons/fasta_clipping_histogram_1.png
M static/fastx_icons/fasta_clipping_histogram_2.png
M static/fastx_icons/fastq_nucleotides_distribution_1.png
M
512 is the unix UID (userid) and GID (groupid) of the user running the
galaxy daemon.
This should be adapted to meet your situation. in our case it is 1009
and 100 for example.
Look it up using :
$ id **the username running galaxy**
best regards
Geert Vandeweyer
On 06/15/2012 03:35 PM,
Hi Matthias,
You uncovered an issue I recently introduced and which I've fixed in change set
7277:4a1389e037c6, which is now running on both public Galaxy tool sheds.
Sorry for the back and forth on this - your line numbers in your paster log
threw me since they were significantly different
Thank you Ross for answering so fast,
I've tried with $i.extra_files_path. When I run my tool, it takes as
argument path/to/database/files/000/dataset_375.files which indeed is the
file that contains the two files I want.
But I still have an error message Cannot open file . So I guess there
On Jun 15, 2012, at 9:05 AM, Peter Cock wrote:
On Fri, Jun 15, 2012 at 12:17 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hello all,
I'm wondering if it is sensible to make Galaxy tools automatically use
the environment variable $NSLOTS to automatically adjust their
number of threads?
On Fri, Jun 15, 2012 at 4:06 PM, Nate Coraor n...@bx.psu.edu wrote:
On Jun 15, 2012, at 9:05 AM, Peter Cock wrote:
On Fri, Jun 15, 2012 at 12:17 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hello all,
I'm wondering if it is sensible to make Galaxy tools automatically use
the
On Jun 15, 2012, at 11:27 AM, Peter Cock wrote:
On Fri, Jun 15, 2012 at 4:06 PM, Nate Coraor n...@bx.psu.edu wrote:
On Jun 15, 2012, at 9:05 AM, Peter Cock wrote:
On Fri, Jun 15, 2012 at 12:17 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hello all,
I'm wondering if it is sensible to
On Fri, Jun 15, 2012 at 4:38 PM, James Taylor ja...@jamestaylor.org wrote:
This is exactly what I think we should do (and have for a long time), but I
think the variable should be something like:
GALAXY_CPUS
(threads is not accurate, a multithread or multiprocess job might want to use
this
New try :
${os.path.join( $input.extra_files_path, 'first_component_file.xxx' )}
${os.path.join( $input.extra_files_path, 'second_component_file.yyy')}
With this, I can see my tool takes as parameters :
myTool path/to/first_component_file.xxx path/to/second_component_file.yyy
This sounds
Hello,
I'm a Galaxy user, and recently have been having trouble uploading my
files to Galaxy via ftp. I've used both Filezilla and Cyberduck, and
have been getting the same error messages:
ftp error 530: too many connections to the client (3)
however, i have disconnected from all ftp
Hi there,
I am piloting my own instance of CloudMan in Amazon Web Services, using
the current public AMI (according to your Wiki), AMI: ami-da58aab3 and
Name: 861460482541/galaxy-cloudman-2011-03-22.
I'd like to either tunnel X11 through SSH (either PuTTY on Windows, or
just at a Linux
Marine,
It seems that the files your tool needs are in the extra_files_path and you
just have to figure out how to get at them for processing.
From my experience, it is trivial to make this work with a wrapper script
in Python.
Given a directory listing of the passed in extra_files_path, you can
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