Hello Sebastian,
Sorry I haven't had a chance to update the tool shed wiki with this
information. I'm not quite done with the implementation (although I'm very
close), so I've held off on the documentation for now. However, here are the
highlights:
My goal is for most of the tool shed repositories ( 90% or more ) to require
inclusion of only an xml file that provides information for installing and
building the tool dependencies. In these cases, the Galaxy framework will
handle the installation, whether it's via fabric or something else. This xml
file must be named tool_dependencies.xml. Here is what this file looks like
for the emboss_5 tool shed repository (I have not yet uploaded this file to the
repository in the main Galaxy tool shed, so you won't find it there at least
for a short wile longer).
=======================
<?xml version="1.0"?>
<tool_dependency>
<package name="emboss" version="5.0.0">
<fabfile>
<method name="install_and_build_package">
<param
name="download_url">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/EMBOSS-5.0.0.tar.gz</param>
<param name="build_commands">
<command>./configure --without-x
--prefix=$INSTALL_DIR</command>
<command>make</command>
<command>make install</command>
</param>
</method>
<method name="install_and_build_package">
<param
name="download_url">ftp://emboss.open-bio.org/pub/EMBOSS/old/5.0.0/PHYLIP-3.6b.tar.gz</param>
<param name ="build_commands">
<command>./configure --without-x
--prefix=$INSTALL_DIR</command>
<command>make</command>
<command>make install</command>
</param>
</method>
</fabfile>
<readme>
These links provide information for building the Emboss package in most
environments .
System requirements
http://emboss.sourceforge.net/download/#Requirements
Platform-dependent notes
http://emboss.sourceforge.net/download/#Platforms
</readme>
</package>
</tool_dependency>
=======================
$INSTALL_DIR is a reserved variable that Galaxy replaces with the installation
directory that is determined at the time the repository and tool dependencies
are being installed.
Notice that the above xml file defines the name of the package to be installed
as well as the version of that package. This information must be found in the
<requirements> tag set of at least 1 of the tool config files within that
downloadable changeset revision of the tool shed repository. So for the
emboss_5 tools configs (e.g., emboss_antigenic.xml, etc), the requirements tag
set looks like this.
<requirements><requirement type="package"
version="5.0.0">emboss</requirement></requirements>
If the dependency name / version information does not match, the tool
dependencies cannot be automatically installed when the Galaxy admin installs
the tool shed repository into their local galaxy instance.
I have several other tool_dependencies.xml examples I can provide if you'd
like. But it might be easer if you send me the tool dependencies for which you
are writing your script and I can provide you the xml definition that will
handle the installation.
The details will be different for those tool shed repositories in which the
owner chooses to include a proprietary fabric script. This these cases, the
<fabfile> tag becomes <proprietary_fabfile>. I have a working prototype for
handling this approach, but things may change slightly before I call it
finished.
I look forward to your response on this. Thanks very much for your interest!
Greg Von Kuster
On Jun 1, 2012, at 12:06 PM, Sebastian J Schultheiss wrote:
> Dear Greg,
>
> according to the Tool Shed wiki page, you will be enabling installation of
> Tool Shed tools with 3rd party dependencies very soon.
>
> Together with Enis Afgan I created several fabric scripts a while ago that
> install some of our tools into an EC2 instance of Galaxy. We are now in the
> process of updating these scripts and wanted to add new ones. Is there
> already a (preliminary) framework that those fabric scripts should follow if
> they are to be packaged in the tool shed repository?
>
> Thanks for your help!
>
> -- Sebastian
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