Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-20 Thread Peter Cock
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

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-19 Thread Peter Cock
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.

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-19 Thread Greg Von Kuster
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.

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-19 Thread Peter Cock
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

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-16 Thread Greg Von Kuster
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

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-15 Thread Peter Cock
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. Neither of

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-15 Thread Greg Von Kuster
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

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-15 Thread Peter Cock
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

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-15 Thread Greg Von Kuster
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

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-15 Thread Peter Cock
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

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-15 Thread Greg Von Kuster
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

Re: [galaxy-dev] environment variables and paths for toolshed tools

2013-02-15 Thread Peter Cock
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

Re: [galaxy-dev] environment variables and paths for toolshed tools

2012-09-18 Thread Greg Von Kuster
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

Re: [galaxy-dev] environment variables and paths for toolshed tools

2012-09-17 Thread Jim Johnson
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

Re: [galaxy-dev] environment variables and paths for toolshed tools

2012-09-16 Thread Jim Johnson
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

Re: [galaxy-dev] environment variables and paths for toolshed tools

2012-09-13 Thread Greg Von Kuster
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

Re: [galaxy-dev] environment variables and paths for toolshed tools

2012-09-12 Thread Greg Von Kuster
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?

Re: [galaxy-dev] environment variables and paths for toolshed tools

2012-09-12 Thread Greg Von Kuster
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