OK..I found a way to allow users to submit as a real users without using
CHOWN...
I did this by:
1) Tweaking the script external_chown_script.py by simply commenting out the
chown statements (see below)
2) Making sure the users are in the same group
3) Setting the umask to 0002 to make all files
Tim,
The Galaxy functional test suite's run time can vary significantly
depending on your environment, and we are currently working on a number
of enhancements to the speed of the functional tests.
You can run the functional tests before installing tools and tool
dependencies, and you can
My apologies, that command was incorrect. The correct version is:
$ sh run_functional_tests.sh help
--Dave B.
On 2/22/13 08:47:19.000, Dave Bouvier wrote:
Tim,
The Galaxy functional test suite's run time can vary significantly
depending on your environment, and we are currently working
Dear all,
For anyone using my Blast2GO for pipelines wrapper:
http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
The newly uploaded v0.0.6 of the wrapper changes from
supporting b2g4pipe v2.3.5 to supporting v2.5 instead.
This is currently available here (while the old v2.3.5
release does not
Hi all,
I've just hit what I consider to be a bug, but may be a design
choice which I don't yet understand: It appears that repository
dependencies cannot refer to other Tool Sheds.
As an example, I want to explore some more complicated
dependency work in my Blast2GO wrapper (I'd like it to be
Hi,
I have an issue with filtering using the Filter tool in the sense that the
first line is considered invalid and I think it has to do with the automatic
guessing of column types.
The condition is like: c4 !='XXX'
The value of c4 for the first line is 'NA'
When the paster.log is checked one
Hi Peter,
As you discovered, repository dependency definitions are currently supported
within a single tool shed. This is a temporary restriction, however, and is
simply due to time / resource constraints. The following section of the tool
shed wiki communicates this.
Il giorno mar, 19/02/2013 alle 20.38 +, Peter Cock ha scritto:
On Tue, Feb 19, 2013 at 6:45 PM, Nicola Soranzo sora...@crs4.it wrote:
Il giorno mar, 19/02/2013 alle 14.15 +, Peter Cock ha scritto:
On Tue, Feb 19, 2013 at 2:00 PM, James Taylor ja...@jamestaylor.org
wrote:
On
On Feb 22, 2013, at 10:21 AM, Shun Liang wrote:
Hi Nate,
After scramble,py failed, I ran
$ python ./scripts/scramble.py -e bx_python
and bx_python seems to be built without any problem:
...
writing build/bdist.linux-armv7l/egg/EGG-INFO/native_libs.txt
creating dist
creating
Hi Marc,
Ah, I think I see the issue here, and it has to do with an assumption being
made that the first line is a undeclared header, which in your case is wrong.
Can you trying adding to your set_meta:
kwd['skip'] = 0
and then restart your sever and then create a new dataset with your
From: Daniel Blankenberg [mailto:d...@bx.psu.edu]
Sent: Friday, February 22, 2013 4:44 PM
To: Marc Logghe
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Filter tool: how to override automatic guessing of
column types ?
Hi Marc,
Ah, I think I see the issue here, and it has to do
Is there a Galaxy XML tool wrapper XSD ?
https://github.com/JeanFred/Galaxy-XSD
I worked more on this XSD. It now passes 181 (and fails on 163)
of the 352 tools packaged in galaxy-dist − it starts being somehow useful.
Many wrappers also use constructs which are not yet documented on the
Hi Nate,
After scramble,py failed, I ran
$ python ./scripts/scramble.py -e bx_python
and bx_python seems to be built without any problem:
...
writing build/bdist.linux-armv7l/egg/EGG-INFO/native_libs.txt
creating dist
creating 'dist/bx_python-0.7.1_7b95ff194725-py2.7-linux-armv7l-ucs4.egg' and
Hi Nate,
After terminating the process which was listening 8080 I am now able to launch
Galaxy.
Many thanks for you help,
Shun
From: Nate Coraor [n...@bx.psu.edu]
Sent: 22 February 2013 15:31
To: Shun Liang
Cc: James Taylor; galaxy-dev@lists.bx.psu.edu
Hi Marc,
You can force the metadata detection to search your entire file by adding a new
set_meta method to your datatype class, e.g. (untested):
def set_meta( self, *args, **kwd ):
kwd['max_data_lines'] = None
kwd['max_guess_type_data_lines'] = None
return super(
On Fri, Feb 22, 2013 at 2:55 PM, Nicola Soranzo sora...@crs4.it wrote:
Il giorno mar, 19/02/2013 alle 20.38 +, Peter Cock ha scritto:
The current minimal implementation you sent me for BLAST+
would be an excellent start. Things like data type sniffers etc
would be a nice to have feature,
On Wed, Feb 20, 2013 at 2:57 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Bumping one of my old queries again, with some more use-cases at the end,
On Wed, Aug 10, 2011 at 11:28 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hi Shun,
Would you please share which third-party tools you are able to compile
on ARM? I'll be very interested in knowing about that. I'm thinking on
things like samtools, bowtie, tophat, cufflinks, bwa, ncbi_blast, etc.
Thanks,
Carlos
On Fri, Feb 22, 2013 at 10:51 AM, Shun Liang
Hello shenwiyn,
You may want to have a look at
http://wiki.galaxyproject.org/Admin/Data%20Integration which provides more
information specific to the indeces/data you'll need and how to install.
Along with data management, that page has instructions on how to download
(via rsync) the same data
Hello,
I am not sure whether this is a bug or a problem with the server, or if it is
just normal but I started a BWA mapping on some paired-end reads of a bacterium
genome two days ago late evening. The job appears in yellow as 'running' but is
it normal that is taking all these hours? I must
Stefano,
Certain jobs have up to 72 hours of run time on the public Main Galaxy
server at https://main.g2.bx.psu.edu (usegalaxy.org). Other sites or
your own site may have other limits.
Jobs last different time lengths in general depending on processing
needs and the capabilities of the
Hi Brad,
I really like this idea. I'm not going to open a ticket yet but talk
with Dan/team about some options. We have an alternate directory
structure modeled from last fall I'd like to get in place before we
start something like this ( is not yet implemented, but it or something
similar
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