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:
http://galaxy-dev.genome.edu.au:9009/";
name="package_velvet_1_2" owner="slugger"
changeset_revision="2c95298637c9" />
$REPOSITORY_INSTALL_DIR
http://www.vicbioinformatics.com/VelvetOptimiser-2.2.5.tar.gz
.
$INSTALL_DIR/bin
$INSTALL_DIR/bin
- your requirments tag in your tool.xml should look like that:
VOPT_SCRIPT_PATH
velvetoptimiser
velvet
I hope it gets a little bit more clear.
Cheers,
Björn
> Respository: velvetoptimiser_gvl -- the main repo.
>
>
> File: velvet_optimiser_vlsci.xml (salient parts)
>
>
> version="1.0.0">
>
> Automatically optimise a de-novo assembly using
> Velvet.
>
>
>
> velvet_optimiser_wrapper_vlsci.pl
>
>\$VOPT_SCRIPT_PATH
>
>'$start_kmer'
>
>'$end_kmer'
>
>'$kmer_step'
>
>
>#for i in $inputs:
>
>'$i.__index__'
>
>'${i.filetype}'
>
> …
>
>
> …
>
>
>
>
>
>
>
> type="set_environment">VOPT_SCRIPT_PATH
>
> version="2.2.5">velvetoptimiser_orphan_225
>
>
>
> …
>
>
>
> File: repository_dependencies.xml
>
>
>
>
>
>
> http://galaxy-dev.genome.edu.au:9009/";
> name="velvetoptimiser_orphan_225" owner="slugger"
> changeset_revision="fc5a642b8741" />
>
>
>
>
>
> Repository: velvetoptimiser_orphan_225
>
>
> File: tool_dependencies.xml
>
>
>
>
>
>
>
>
> action="set_to">$REPOSITORY_INSTALL_DIR
>
>
>
>
>
>
>
>
> type="download_by_url">http://www.vicbioinformatics.com/VelvetOptimiser-2.2.5.tar.gz
>
>
>
>.
>
>
> $INSTALL_DIR/bin
>
>
>
>
>
> action="prepend_to">$INSTALL_DIR/bin
>
>
>
>
>
>
>
>
>
>
>
>
> File: repository_dependencies.xml
>
>
>
>
>
>
> http://galaxy-dev.genome.edu.au:9009/";
> name="velvet_1208" owner="slugger"
> changeset_revision
