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bcgsc / tigmint

⛓ Correct misassemblies using linked AND long reads
https://bcgsc.github.io/tigmint/
GNU General Public License v3.0
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Fix path. Never hardcode a path, use long-to-linked-pe from PATH instead #127

Closed ccoulombe closed 9 months ago

ccoulombe commented 9 months ago

Use long-to-linked-pe from $PATH instead. Never never hardcode a path.

lcoombe commented 9 months ago

Thanks for your contributions @ccoulombe! Currently, things are installed in such a way that we look for this file relative to the installation of other scripts. We recognize this is non-ideal, and have it on our radar to put long-to-linked-pe in btllib, but I can't give a timeline for when that will happen unfortunately.

ccoulombe commented 9 months ago

Using the script/binary/file from a virtual environment bin folder which is in the $PATH, or simply asking where to find the executable using which ease the puzzle of using relative installation paths.

lcoombe commented 9 months ago

Thanks @ccoulombe! As discussed, I prefer to retain the current long-to-linked-pe path behaviour, but use the long-to-linked-pe found on the PATH, if applicable - See #128. I have not changed the tests for now, as that is for our own continuous integration - the provided test demo bash script is what to use if you would like to test your installation.