Can't change working directory during tool dependency installation
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
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 <bgrande@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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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? Best regards, Bruno On Fri, Oct 24, 2014 at 11:52 PM, Ross <ross.lazarus@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 <bgrande@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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