You might need to specify multiple command lines in a single shell action -
separated by ; like:
cd foo; perl foo bah; more something; cleanup
Otherwise you might just find yourself back in the temp installation
directory after each separate action


Ross Lazarus
Head, Computational Biology, Baker IDI, Melbourne, Australia
Pubs: http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ


On Sat, Oct 25, 2014 at 4:10 PM, Bruno Grande <bgra...@sfu.ca> wrote:

> I originally posted this question <https://biostar.usegalaxy.org/p/9401/>
> on the Galaxy Biostars, but later realized that galaxy-dev is probably more
> appropriate. So, here it goes.
>
> I'm trying to automate the installation of a tool's dependency with a tool
> dependency definition repository. During the package installation process,
> after moving the contents of a downloaded archive to the installation
> directory (*i.e.* $INSTALL_DIR), I simply want to change to that target
> directory away from the initial temporary working directory.
>
> However, I can't seem to change directory, either with a change_directory
> action or a cd shell_command action. Running pwd before and after
> attempting to change directory confirms this (see attached for installation
> log). I even made sure that $INSTALL_DIR is different from my initial
> working directory.
>
> Best regards,
> Bruno
>
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