I missed that $__tool_directory__ in the docs. thanks John!
Brad -- Brad Langhorst, Ph.D. Applications and Product Development Scientist
On Mar 26, 2015, at 1:12 PM, John Chilton jmchilton@gmail.com wrote:
Brad,
Yes - that environment variable trick is an anti-pattern in my mind because it is heavy and because it only works for tool shed installed tools. As of 15.03 you can now just use $__tool_directory__ to refer to the directory the tool is in. I can point at the patch if you want to back port this to an older Galaxy (the patch is relatively small).
Planemo's building a tool documentation has a section on writing wrapper scripts that demonstrates the use of the new $__tool_directory__ variable - http://planemo.readthedocs.org/en/latest/writing_standalone.html#wrapping-a-....
Hope this helps, -John
On Thu, Mar 26, 2015 at 1:06 PM, Langhorst, Brad Langhorst@neb.com wrote:
I’m working on a very simple tool.
<tool id="gc_stat" name="GC Stat" version="0.1.0"> <requirements> <requirement type="binary">Rscript</requirement> <requirement type="package" version="1.1">samtools</requirement> <requirement type="package" version="3.0.3">R</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio>
<command><![CDATA[ samtools view $bam | Rscript simple_script.R > $output ]]></command>
<inputs> <param name='bam' type='data' format='bam' label='Mapped reads' help='BAM files'/> </inputs> <outputs> <data format='tabular' name='output' label='GC Statistic on ${on_string}'/> </outputs> <help><![CDATA[ Calculates a GC statistic for the specified BAM file. ]]></help> </tool>
this won’t work because Rscript is not running in the tool install directory and can’t find simple_script.R…
I’ve just been reading
https://trello.com/c/9lQ7Sr8I/636-galaxy-tool-enhancement-to-accommodate-rep...
and it seems that I have to add another file…
<?xml version="1.0"?>
<tool_dependency> <set_environment version="1.0"> <environment_variable name="TOOL_INSTALL_DIR" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> </tool_dependency>
and add a set_enviornment dependency to bring it in.
<requirements> ... <requirement type="set_environment">TOOL_INSTALL_DIR</requirement> </requirements> <command><![CDATA[ samtools view $bam | Rscript $TOOL_INSTALL_DIR/simple_script.R > $output ]]></command>
I did that but the tool still won’t execute, in fact the . Maybe because I have to put this into a toolshed - or maybe I’ve done something wrong?
I think this complexity could be avoided by setting an TOOL_INSTALL_DIR environment var as a tool is executed (though John doesn’t seem to like that idea due to a responsibility mixing issue)
I think it’s a worthy goal to make tool development as frictionless as possible. Is there a simpler way to do this?
Brad
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