Hi Simon!
> Hi all,
>
> I've been trying to get my velvet optimiser wrapper to automatically
> install the tool and its dependencies to no avail.
Nice!
> Here is my problem in detail.
> I have what I thought would be a simple wrapper and tool to pack into
> the new toolshed.
>
>
> I have a tool_wrapper which points to a perl tool (VelvetOptimiser.pl)
> which in turn depends on some binaries being installed (velveth and
> velvetg). When I try and load these with tool dependencies and
> repository dependencies, galaxy cannot find the VelvetOptimiser.pl
> script nor the velvet binaries after they have been installed.
> (They're there, I've checked.)
> It comprises of a repository (velvetoptimiser_gvl) with:
Are you installing your velvetoptimiser.pl (copying to some location) or
is it shipped with your repository?
In the first case you do not need the "VOPT_SCRIPT_PATH" because its
part of your PATH, in the latter case you do not need to install it.
> velvet_optimiser_vlsci.xml which points to a more complex
> velvet_optimiser_vlsci_wrapper.pl to create the actual command line.
> (This works when the dependencies are installed on the machine and
> available in the galaxy users path).
>
>
> A repository_dependencies.xml file which points to an orphan
> repository (velvetoptimiser_orphan_225)
Please name your repositories according to the naming scheme. Something
like package_depname_majorversion_minorversion (like package_atlas_3_10,
package_bwa_0_6_2, package_numpy_1_7).
>
> velvetoptimiser_orphan_225 has a tool_dependencies.xml to install the
> VelvetOptimiser.pl and associated modules and a
> repository_dependencies.xml file to point to the velvet orphan
> repository (velvet_1208).
> velvet_1208 has a tool_dependencies.xml file which clones, installs
> and makes the velvet binaries and puts them in the right place.
> All of the installations work when you install the tool from the
> toolshed. However, when I go to run the tool, it kept coming back
> saying it couldn’t find the VelvetOptimser.pl file. Then after the
> documentation was updated, I thought I may have to include the path as
> an environment like in the R_SCRIPT_PATH example in the wiki. So I set
> that up as well to no avail. I’ve left it in the files attached..
> Both the toolshed that these repos are in and the galaxy being
> installed into are the latest versions as of 05/06/2013.
I think you miss used the repository_dependencies.xml file.
Try to following:
- one orphan-tool-definition called package_velveth_1_2 (assuming 1_2 is
stable and in point releases no new features are introduced, only
bugfixed). Insert you velveth install script.
- place the following (please adopt, its not tested) in your main
repository:
<?xml version="1.0"?>
<package name="velvet" version="0.1.18">
<repository toolshed="http://galaxy-dev.genome.edu.au:9009/";
name="package_velvet_1_2" owner="slugger"
changeset_revision="2c95298637c9" />
</package>
<tool_dependency>
<!-- im not sure that is needed, see above -->
<set_environment version="1.0">
<environment_variable name="VOPT_SCRIPT_PATH"
action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
</set_environment>
<package name="velvetoptimiser" version="2.2.5">
<install version="1.0">
<actions>
<action
type="download_by_url">http://www.vicbioinformatics.com/VelvetOptimiser-2.2.5.tar.gz</action>
<action type="move_directory_files">
<source_directory>.</source_directory>
<destination_directory>$INSTALL_DIR/bin</destination_directory>
</action>
<action type="set_environment">
<environment_variable name="PATH"
action="prepend_to">$INSTALL_DIR/bin</environment_variable>
</action>
</actions>
</install>
</package>
</tool_dependency>
- your requirments tag in your tool.xml should look like that:
<requirments>
<requirement
type="set_environment">VOPT_SCRIPT_PATH</requirement>
<requirement type="package"
version="2.2.5">velvetoptimiser</requirement>
<requirement type="package" version="0.1.18">velvet</requirement>
</requirments>
I hope it gets a little bit more clear.
Cheers,
Björn
> Respository: velvetoptimiser_gvl -- the main repo.
>
>
> File: velvet_optimiser_vlsci.xml (salient parts)
>
>
> <tool id="velvetoptimiser_vlsci" name="Velvet Optimiser vlsci"
> version="1.0.0">
>
> <description>Automatically optimise a de-novo assembly using
> Velvet.</description>
>
> <command interpreter="perl">
>
> velvet_optimiser_wrapper_vlsci.pl
>
> \$VOPT_SCRIPT_PATH
>
> '$start_kmer'
>
> '$end_kmer'
>
> '$kmer_step'
>
>
> #for i in $inputs:
>
> '$i.__index__'
>
> '${i.filetype}'
>
> …
>
>
> …
>
> </outputs>
>
>
>
> <requirments>
>
> <requirement
> type="set_environment">VOPT_SCRIPT_PATH</requirement>
>
> <requirement type="package"
> version="2.2.5">velvetoptimiser_orphan_225</requirement>
>
> </requirments>
>
> …
>
>
>
> File: repository_dependencies.xml
>
>
> <?xml version="1.0"?>
>
> <repositories description="Velvet Optimiser requires access to the
> VelvetOptimiser package.">
>
> <repository toolshed="http://galaxy-dev.genome.edu.au:9009/";
> name="velvetoptimiser_orphan_225" owner="slugger"
> changeset_revision="fc5a642b8741" />
>
> </repositories>
>
>
>
> Repository: velvetoptimiser_orphan_225
>
>
> File: tool_dependencies.xml
>
>
> <?xml version="1.0"?>
>
> <tool_dependency>
>
> <set_environment version="1.0">
>
> <environment_variable name="VOPT_SCRIPT_PATH"
> action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
> </set_environment>
>
> <package name="VelvetOptimiser-2.2.5" version="2.2.5">
>
> <install version="1.0">
>
> <actions>
>
> <action
> type="download_by_url">http://www.vicbioinformatics.com/VelvetOptimiser-2.2.5.tar.gz</action>
>
> <action type="move_directory_files">
>
> <source_directory>.</source_directory>
>
>
> <destination_directory>$INSTALL_DIR/bin</destination_directory>
>
> </action>
>
> <action type="set_environment">
>
> <environment_variable name="PATH"
> action="prepend_to">$INSTALL_DIR/bin</environment_variable>
>
> </action>
>
> </actions>
>
> </install>
>
> </package>
>
> </tool_dependency>
>
>
> File: repository_dependencies.xml
>
>
> <?xml version="1.0"?>
>
> <repositories description="Velvet Optimiser requires access to the
> velvet binaries.">
>
> <repository toolshed="http://galaxy-dev.genome.edu.au:9009/";
> name="velvet_1208" owner="slugger"
> changeset_revision="2c95298637c9" />
>
> </repositories>
>
>
> Repository: velvet_1208
>
>
> File: tool_dependencies.xml
>
>
> <?xml version="1.0"?>
>
> <tool_dependency>
>
> <package name="velvet" version="1.2.08">
>
> <install version="1.0">
>
> <actions>
>
> <action type="shell_command">git clone
> git://github.com/dzerbino/velvet.git</action>
>
> <action type="shell_command">make -i CATEGORIES=4
> MAXKMERLENGTH=191 OPENMP=1</action>
>
> <action type="move_file">
>
> <source>velvetg</source>
>
> <destination>$INSTALL_DIR/bin</destination>
>
> </action>
>
> <action type="move_file">
>
> <source>velveth</source>
>
> <destination>$INSTALL_DIR/bin</destination>
>
> </action>
>
> <action type="set_environment">
>
> <environment_variable name="PATH"
> action="prepend_to">$INSTALL_DIR/bin</environment_variable>
>
> </action>
>
> </actions>
>
> </install>
>
> <readme>
>
> Installs velvet latest version. (called 1.2.08 for Galaxy
> purposes.)
>
> </readme>
>
> </package>
>
> </tool_dependency>
>
>
>
>
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___________________________________________________________
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