Hello,
I am developing a new galaxy tool based on R language.
My tool uses R 3.1.2 and it is dependent from a number of libraries.
I deployed my tool in the testtoolshed but It does not find the R libraries when I try to install it from the shed.
What is it wrong in the following tool_dependencies.xml?
<?xml version="1.0"?>
<tool_dependency>
<package name="R" version="3.1.2">
<repository name="package_r_3_1_2" owner="iuc" prior_installation_required="True" />
</package>
<package name="mytoolname" version="1.0">
<install version="1.0">
<actions>
<action type="setup_r_environment">
<repository name="package_r_3_1_2" owner="iuc">
<package name="R" version="3.1.2" />
</repository>
<package sha256sum="d451f2c72c46a7b5fa6dd252a207ba72f0a5a86d1bfc95408935f079efa85f77">
https://depot.galaxyproject.org/software/BiocGenerics/BiocGenerics_0.12.1_src_all.tar.gz
</package>
<package sha256sum="7585cd13b5ae6c3dd918327803de4918dcc11cf6bea45df4e5051c492e49db2a">
https://depot.galaxyproject.org/software/Biobase/Biobase_2.26.0_src_all.tar.gz
</package>
<package sha256sum="f3e9781e84e114b7a88eb099825936cc5ae7276bbba5af94d35adb1b3ea2ccdd">
https://depot.galaxyproject.org/software/RColorBrewer/RColorBrewer_1.1-2_src_all.tar.gz
</package>
<package sha256sum="011131ed104f5be2eed7d7387877e2fe70c1ac72c1052de12cd2284cb61ce2b3">
https://depot.galaxyproject.org/software/limma/limma_3.22.6_src_all.tar.gz
</package>
<package sha256sum="4b7fd5c6c1358a7e4c32c10237aa6f3f5279585afef83b0ffa1b3fc74c5f3006">
https://depot.galaxyproject.org/software/BBmisc/BBmisc_1.9_src_all.tar.gz
</package>
<package>https://bioarchive.galaxyproject.org/HTqPCR_1.20.0.tar.gz</package>
<package>https://bioarchive.galaxyproject.org/RankProd_2.38.0.tar.gz</package>
<package>https://bioarchive.galaxyproject.org/impute_1.40.0.tar.gz</package>
</action>
<action type="set_environment">
<environment_variable action="set_to" name="MYTOOLNAME_ROOT_PATH">$INSTALL_DIR</environment_variable>
</action>
</actions>
</install>
<readme>
Set up of R environment.
</readme>
</package>
</tool_dependency>