I think a working example that uses this pattern is Bjoern's glimmer tool:
The only obvious difference I see that he sets the environment
variable to $REPOSITORY_INSTALL_DIR in tool_dependencies.xml
changing that fix anything? He also escapes the environment variable
in the command \$R_SCRIPT_PATH instead of $R_SCRIPT_PATH in your case.
I find set_environment to be something of an anti-pattern myself - it
doesn't map well to other packaging systems such as nix or brew. I
think it would be better to resolve things relative to the script from
the script itself or to write out a helper script that wraps up R and
stuff and resolve paths relative to itself but I guess that is beside
On Sat, Oct 25, 2014 at 3:38 PM, Jeremy Liu <jeremy....@yale.edu> wrote:
> Hi Galaxy Dev,
> Been having trouble getting my Galaxy tools to work with the testtoolshed.
> Here is the tools repository:
> In particular, I've been focusing on getting the
> region_motif_intersect.r script to work properly when installed from
> the testtoolshed. intersect.r runs using files located in the same
> location as where the repository is installed, in the folder
> region_motif_db. To make sure that the tool knows where these files
> are, I've been trying to pass the repository install location as an
> argument in the r script invocation (see region_motif_intersect.xml
> and tool_dependencies.xml) .
> To set the repository install location in the environment, I've been
> basing off of this wiki entry:
> When I install the repository to my local Galaxy, it gives me the
> following warnings:
> galaxy.tools.deps DEBUG 2014-10-25 15:12:35,376 Building dependency
> shell command for dependency 'R_SCRIPT_PATH'
> galaxy.tools.deps WARNING 2014-10-25 15:12:35,377 Failed to resolve
> dependency on 'R_SCRIPT_PATH', ignoring
> Then when I run the tool from Galaxy, this is the run command:
> export PACKAGE_BASE; .
> --args $R_SCRIPT_PATH p
> What exactly is going on here? How do I make sure my tool knows where
> the reference files it needs are, since it won't be in the job working
> Note: the files that intersect.r needs are not in the toolshed
> repository, since they are a few GB. I was planning on providing that
> as a separate download or using the Data Managers to solve the
> problem. But as long as I can get the tool to look for it in that
> folder, that would be perfect.
> Jeremy Liu
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> To search Galaxy mailing lists use the unified search at:
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at: