Initial implementation of "planemo depbash" #310
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TODO: - Testing - Escaping/quoting filenames - Implement missing actions - Exceptions rather than errors as bash commands? - Expose as a planemo command
Running "bash install.sh" would not alter environment variables in the caller's scope. Using "source install.sh" does alter the caller's environment variables, but "exit" or any error in strict mode will end the user's terminal session. Idea here is "bash install.sh" will download and install the tool, and also create "env.sh" for use in "source env.sh" within the Galaxy tool dependency framework.
Was going to call this 'planemo shed2bash' or similar, but easier to run the installation from Python than writing a bash script?
Also wrap env actions as conditional.
This is going to be very useful while working on implementing the rest of 'planemo depbash'.
TODO: Also use an MD5 checksum of the URL here?
Implementing this will be tricky...
This was important as the installation script would often change directory (especially into a temp working directory) from where the curl command would fail as the relative path to the download cache no longer existed.
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After some frustration leading to this hack peterjc@7073505 I finally got the basic tests to pass on TravisCI. Should I do any branch history cleanup, or leave this as it is for any merge? |
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Minor update to fix the tests since the contents of @jmchilton Would you prefer a cleaned-up history? Or just do a |
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My preference would be this be squashed into a single commit with a nice commit message if you are offering 😄, I don't really enforce this and don't always do it myself and so I have no problem with it being merged as is. |
peterjc
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Oct 7, 2015
This is a squashed commit of pull request #310 for issue #303, for converting tool_dependencies.xml install recipes into bash scripts. There is a lot that could be done better, or added, including: - refactor to use a visitor pattern instead of my .to_bash() methods - expand the command line API with options for paths and filenames - setting defaults like download cache via ~/.planemo.yml - complete the action coverage (especially the R/Python/Perl environments) - avoid collisions in the download cache which currently assumes unique filenames However, this is enough to help with automating dependency installation in a continuous integration setup like TravisCI.
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Thanks @jmchilton - done as a squashed merge: f798c7e |
This was referenced Oct 7, 2015
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As described on issue #303, this implements a new
planemo depbashcommand for convertingtool_dependencies.xmlinstall recipes into bash scripts.There is a lot that could be done better, or added, including:
.to_bash()methodsIs this suitable to merge as is, or does it need further work?
Does anyone have a better idea for the command name? I have no strong attachment to "depbash" (dependencies to bash script).
I have no objections to squashing down the git commit history here.
P.S. I have considered determining dependencies is out of scope for this work.