Command to convert tool_dependencies.xml recipes into shell scripts #303
Description
Related to #19 (testing tool_dependencies.xml without a tool shed), I would like to be able to run an install recipe from a tool_dependencies.xml file locally and/or turn it into a simple shell script for the current platform.
(The platform specific actions could be turned into bash if statements if preferred)
This seems to overlap with https://github.com/jmchilton/shed2tap
e.g. https://github.com/peterjc/pico_galaxy/blob/master/tools/effectiveT3/tool_dependencies.xml
<?xml version="1.0"?>
<tool_dependency>
<package name="effectiveT3" version="1.0.1">
<install version="1.0">
<actions>
<!-- Set environment variable so Python script knows where to look -->
<action type="set_environment">
<environment_variable name="EFFECTIVET3" action="set_to">$INSTALL_DIR</environment_variable>
</action>
<!-- Main JAR file -->
<action type="shell_command">wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_GUI-1.0.1.jar</action>
<!-- If using action type download_file will need to move the file,
<action type="move_file"><source>TTSS_GUI-1.0.1.jar</source><destination>$INSTALL_DIR/</destination></action>
-->
<!-- Three model JAR files -->
<action type="make_directory">$INSTALL_DIR/module</action>
<action type="shell_command">wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_ANIMAL-1.0.1.jar</action>
<action type="move_file"><source>TTSS_ANIMAL-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action>
<action type="shell_command">wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_PLANT-1.0.1.jar</action>
<action type="move_file"><source>TTSS_PLANT-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action>
<action type="shell_command">wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_STD-1.0.1.jar</action>
<action type="move_file"><source>TTSS_STD-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action>
<action type="shell_command">wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_STD-2.0.1.jar</action>
<action type="move_file"><source>TTSS_STD-2.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action>
</actions>
</install>
<readme>
Downloads effectiveT3 v1.0.1 and the three models from http://effectors.org/ aka http://effectors.csb.univie.ac.at/
</readme>
</package>
</tool_dependency>
Would become something like this (assuming already in install directory as per XML convention):
#!/bin/bash
#House keeping: strict bash mode, etc
set -euo pipefail
export INSTALL_DIR=$PWD
#Start of conversion from XML recipe:
echo "Installing effectiveT3 version 1.0.1"
export EFFECTIVET3=$INSTALL_DIR
wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_GUI-1.0.1.jar
mkdir $INSTALL_DIR/module
wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_ANIMAL-1.0.1.jar
mv TTSS_ANIMAL-1.0.1.jar $INSTALL_DIR/module/
wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_PLANT-1.0.1.jar
mv TTSS_PLANT-1.0.1.jar $INSTALL_DIR/module/
http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_STD-1.0.1.jar
mv TTSS_STD-1.0.1.jar $INSTALL_DIR/module/
wget http://effectors.csb.univie.ac.at/sites/eff/files/others/TTSS_STD-2.0.1.jar
mv TTSS_STD-2.0.1.jar $INSTALL_DIR/module/
I would then be able to run this within TravisCI with the advantages that the install recipe is not repeated (tool_dependencies.xml and .travis.yml) and moreover I would actually be able to test tool_dependencies.xml, e.g. peterjc/pico_galaxy@243311c