Dear Björn,
Is not it what I did?
I wrote requirement type=package version=1.7.1numpy/requirement
in test.xml, and the version number is the same as yours...
Many thanks again,
Matthias.
On Thu, 25 Apr 2013, Björn Grüning wrote:
Hi Matthias,
you need to add something like the following
Hi Matthias,
you need to add something like the following to your tool defintion:
requirements
requirement type=package version=1.1p1chemfp/requirement
/requirements
The version and the name needs to be the same as in your
tool_dependency.xml.
Cheers,
Bjoern
Björn,
I have galaxy-dist.
Hi Matthias,
Sure,
This is the least I can do. However, I do not know how to install a
package from a simple XML, and without Tool Shed installed repository.
it's documented here:
http://wiki.galaxyproject.org/Tool%
Dear everyone,
I finally got the answer. The append_to does not seem do work in the
tool_dependencies.xml:
---
environment_variable name=PYTHONPATH
action=append_to$REPOSITORY_INSTALL_DIR/environment_variable
---
does not insert anything, while:
---
environment_variable name=PYTHONPATH
Sure,
This is the least I can do. However, I do not know how to install a
package from a simple XML, and without Tool Shed installed repository.
I will check that.
I have downloaded Galaxy for installation less than a week ago.
Matthias.
On Wed, 24 Apr 2013, Björn Grüning wrote:
Hi
Björn,
I have galaxy-dist. Was it the right choice?
Here is what I did. I copied your tool_dependencies.xml into my project
(s_mart, in the test Tool Shed), and I created a testing XML file, which
uses your dependencies:
---
tool id=test name=test
descriptionThis is a
Hi Matthias,
PYTHONPATH will not be changed globally.
It's only changed during execution of your tool.
Have a look under ./tool_deps/.../.../.../s_mart/ there is a file called
env.sh with your PYTHONPATH.
That file is executed before your command
commandenv $outputFile/command
is executed.
Hi Matthias,
Dear Björn,
Maybe the problem is here. I cannot find neither tool_deps, nor
env.sh.
The install is fresh from yesterday... I should check why I did not
generate these files.
By the way, if env.sh is sourced right before my script, I should see
the updated PYTHONPATH in the
Dear Björn,
Maybe the problem is here. I cannot find neither tool_deps, nor
env.sh.
The install is fresh from yesterday... I should check why I did not
generate these files.
By the way, if env.sh is sourced right before my script, I should see
the updated PYTHONPATH in the result of the
On Tue, Feb 19, 2013 at 12:06 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Feb 19, 2013 at 11:39 AM, Greg Von Kuster g...@bx.psu.edu wrote:
On Feb 19, 2013, at 5:10 AM, Peter Cock wrote:
Yes, the complete directory hierarchy and content of the original
repository revision is
On Sat, Feb 16, 2013 at 9:41 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
Thanks for your thoughts on this. I've created the following Trello card for
this enhancement.
Hi Peter, see below...
On Feb 19, 2013, at 5:10 AM, Peter Cock wrote:
On Sat, Feb 16, 2013 at 9:41 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
Thanks for your thoughts on this. I've created the following Trello card
for this enhancement.
On Tue, Feb 19, 2013 at 11:39 AM, Greg Von Kuster g...@bx.psu.edu wrote:
On Feb 19, 2013, at 5:10 AM, Peter Cock wrote:
Yes, the complete directory hierarchy and content of the original
repository revision is preserved when it installed into Galaxy.
Based on a sample of one, it seems the
Hi Peter,
Thanks for your thoughts on this. I've created the following Trello card for
this enhancement.
https://trello.com/card/galaxy-tool-enhancement-to-accommodate-repository-install-dir/506338ce32ae458f6d15e4b3/636
The priority for the tool shed in the area of tool dependencies like this
Hello Peter, please see my response at the end.
On Feb 15, 2013, at 6:47 AM, Peter Cock wrote:
On Sep 12, 2012, at 1:00 PM, David Hoover wrote:
Are there any environment variables that are honored by toolshed installed
tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or
On Fri, Feb 15, 2013 at 4:05 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi guys,
Reading the rest of the thread from December, Greg's new code did
get checked in and should be working (I've not tried this yet).
However, I can't help feeling that defining the two environment variables
David
Hi Peter,
On Feb 15, 2013, at 11:14 AM, Peter Cock wrote:
On Fri, Feb 15, 2013 at 4:05 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi guys,
Reading the rest of the thread from December, Greg's new code did
get checked in and should be working (I've not tried this yet).
However, I can't
On Fri, Feb 15, 2013 at 4:32 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Usecase: Tool comes with a simple datafile (e.g. defining a search motif,
say motif.dat) which is used by a script (say motif.py) via a normal
Galaxy tool XML file (say motif.xml).
Perhaps I can just put my data file
On Feb 15, 2013, at 11:45 AM, Peter Cock wrote:
On Fri, Feb 15, 2013 at 4:32 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Usecase: Tool comes with a simple datafile (e.g. defining a search motif,
say motif.dat) which is used by a script (say motif.py) via a normal
Galaxy tool XML file (say
On Fri, Feb 15, 2013 at 4:57 PM, Greg Von Kuster g...@bx.psu.edu wrote:
On Feb 15, 2013, at 11:45 AM, Peter Cock wrote:
Actually for the example I am working on, the motif.py script would be
the tool executable, called from motif.xml like this:
command interpreter=pythonmotif.py $fasta_file
Hi Nate,
I am sorry I missed your reply... Thanks for your input, will try this
soon.
Cheers,
Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 02/13/2013 06:31 PM, Nate
On Feb 11, 2013, at 7:48 AM, Joachim Jacob |VIB| wrote:
Hello all,
After a *reboot* of our Galaxy server, the environment variables are set
correctly.
However, after *restarting* the Galaxy process on a running server, by
logging in as Galaxy and running the init script on CentOS as
To: David Hoover hoove...@helix.nih.gov
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] environment variables and paths for toolshed
tools
Message-ID: f75d6320-3af8-4bb0-8f31-b0f44aa13...@bx.psu.edu
Content-Type: text/plain; charset=us-ascii
Hello David,
I've just committed change
Subject: Re: [galaxy-dev] environment variables and paths for toolshed
tools
Message-ID:f75d6320-3af8-4bb0-8f31-b0f44aa13...@bx.psu.edu
Content-Type: text/plain; charset=us-ascii
Hello David,
I've just committed change set 7656:6aadac8026cb to the Galaxy central
repository that provides
To: David Hooverhoove...@helix.nih.gov
Cc:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] environment variables and paths for toolshed
tools
Message-ID:f75d6320-3af8-4bb0-8f31-b0f44aa13...@bx.psu.edu
Content-Type: text/plain; charset=us-ascii
Hello David,
I've just committed change
Hello David,
I've just committed change set 7656:6aadac8026cb to the Galaxy central
repository that provides the ability to do what you need here. It would be
great if you could try things out and let me know if you run into any problems.
I've been working with nikhil-joshi's
Hello David,
This is not currently possible, but will be available in the next Galaxy
distribution release, currently scheduled for about 10 days from now. You will
include a tool_dependencies.xml file in your tool shed repository that looks
something like the following.
?xml version=1.0?
Hi David,
With the exception of requiring versions strings in requirement tags in the
tool config in order to enable versioned tool dependency installation (which is
documented in the tool shed wiki at
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