Refactor #4
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Refactor #4
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also download other files in parts to prevent failed ftp downloads and check for existing files that are non .gz
…input to SLURM jobs
Add probe settings to the config file and add a cli command to run probe design in parallel on slurm
Added usage instructions for SLURM and local execution.
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The code has been reorganised into a set of submodules within the folder multi_padlock_design.
CLI entry points have been added which enable automatic download of BLAST databases and associated data, as well as ways to run the pipeline as parallel jobs on slurm or locally.
The README has been updated to reflect the new layout of the pipeline and how a user can interact with it.
I've tried to ensure all imports are fixed, even for the snail probe design but I haven't tested the snail probe side of things.
I have tested:
Known issue:
Giving a csv with more than one gene will break the local pipeline due to indexing errors. (Current extensions to the pipeline were built around the assumptions of running this always on SLURM for single genes per job).
This issue is listed here: #3
It doesn't affect the intended SLURM use of the pipeline, so I would suggest merging and then fixing this issue later (for external users who don't have access to HPC resources)