Stringing commands together in a single shell_command action seems to be a
good workaround. Thanks!
On the other hand, I wonder if this is the expected behaviour. Wouldn't it
defeat the purpose of having a change_directory action, given that the
current working directory changes back to the initial temporary directory
as soon as the action is done?
On Fri, Oct 24, 2014 at 11:52 PM, Ross <ross.laza...@gmail.com> wrote:
> 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,
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