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Detect binaries automatically if they are in the PATH #4

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guma44 opened this issue Dec 10, 2020 · 1 comment
Open

Detect binaries automatically if they are in the PATH #4

guma44 opened this issue Dec 10, 2020 · 1 comment
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enhancement New feature or request

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@guma44
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guma44 commented Dec 10, 2020

Path to Salmon binary is now hardcoded. It would be better when PISCES would check if salmon is in the PATH eg. like here https://stackoverflow.com/questions/377017/test-if-executable-exists-in-python.

@mdshw5
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mdshw5 commented Dec 14, 2020

I think this is a great idea, but would also like to fall back on bundling a version of salmon that works with PISCES. Some of the older versions (< 1.0) are incompatible with genome-centric transcriptome indexing. I'll consider how this might be implemented.

@mdshw5 mdshw5 self-assigned this Dec 14, 2020
@mdshw5 mdshw5 added the enhancement New feature or request label Dec 14, 2020
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