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bokulich-lab / q2-fondue

Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere
BSD 3-Clause "New" or "Revised" License
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FIX: correctly install sra-toolkit during conda build #126

Closed misialq closed 2 years ago

misialq commented 2 years ago

Adjusts the sra-toolkit installation script to use the PREFIX env variable when available (i.e., during conda builds) or CONDA_PREFIX when installing in an existing, activated conda environment.

Testing: to test, one needs to build the conda package locally and then install the built package in a fresh environment (I did that, all worked). It will be much easier to test after merging, once the CI takes care of the build process :)

misialq commented 2 years ago

Thanks @lina-kim, good question! No, if you follow the current README instructions, technically, this installation has not much to do with conda builds. However, the adjustment in this PR allows for building conda packages that will take care of the SRA-Toolkit so that the user never again needs to care about our installation script (i.e., you will just do conda install q2-fondue and tada! all is there). I have not updated the README yet as I want to first do a final test to check that everything works as expected (this is, however, only possible after merging) - there'll be a follow up PR most likely.