On Tue, Feb 19, 2013 at 12:06 PM, Peter Cock wrote:
> On Tue, Feb 19, 2013 at 11:39 AM, Greg Von Kuster 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 Galax
On Tue, Feb 19, 2013 at 11:39 AM, Greg Von Kuster 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 installation
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 wrote:
>> Hi Peter,
>>
>> Thanks for your thoughts on this. I've created the following Trello card
>> for this enhancement.
>>
>> https://trello.com/card/galaxy-tool-enha
On Sat, Feb 16, 2013 at 9:41 PM, Greg Von Kuster wrote:
> 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
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
On Fri, Feb 15, 2013 at 4:57 PM, Greg Von Kuster 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:
>>
>> motif.py $fasta_file $tabular_file
>>
>> i.e. A compl
On Feb 15, 2013, at 11:45 AM, Peter Cock wrote:
> On Fri, Feb 15, 2013 at 4:32 PM, Greg Von Kuster 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 (
On Fri, Feb 15, 2013 at 4:32 PM, Greg Von Kuster 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
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 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
On Fri, Feb 15, 2013 at 4:05 PM, Greg Von Kuster 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
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
>> 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
>> $GALAXY_HOME, then uploaded it the test toolshed, then installed it
>> automatically. Nei
n't yet looked at the repository code to see how that might happen.
>>
>>
>> Pablo,
>>
>> The http://sourceforge.net/projects/snpeff/files/ repository should
>> probably have versions packaged for download named like:
>>
>> http
014298767 Aug 23 12:17 snpEff_3_0/SnpSift.jar
...
That will allow versioning within galaxy, and successive versions of
tool_dependencies.xml with only need a change to the action tag:
download_by_url
Thanks,
JJ
I'm trying to test a repository that use in tool_depen
Messa
change to the action tag: download_by_url
Thanks,
JJ
I'm trying to test a repository that use in tool_depen
Message: 18
Date: Thu, 13 Sep 2012 11:46:32 -0400
From: Greg Von Kuster
To: David Hoover
Cc:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] environment variables and paths for
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 deseq_and_sam2
Hi David,
With the exception of requiring versions strings in tags in the
tool config in order to enable versioned tool dependency installation (which is
documented in the tool shed wiki at
http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_third-party_tool_dependency_installation_and_compilation
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.
$INSTA
Are there any environment variables that are honored by toolshed installed
tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or
$GALAXY_HOME, then uploaded it the test toolshed, then installed it
automatically. Neither of these resolved to what I expected. I don't want to
har
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