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It is safe to assume that the user has correctly set up guix in their PATH.
* README.md: Disuse absolute paths to guix in command invocations.
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guix-bioinformatics is a Guix channel that is set up by `guix pull'. There is
no need to specify it explicitly using GUIX_PACKAGE_PATH.
* README.md: Do not explicitly set GUIX_PACKAGE_PATH for any command.
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heatmap_generation
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* Provide documentation on downloading and using the genotype files.
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* README.md: update header: Traits ==> Trait
* gn3/computations/qtlreaper.py: update header: Traits ==> Trait
* qtlfilesexport.py: Choose only BXD strains
Rename the first column header from "Traits" to "Trait" to correspond with
what `rust-qtlreaper` expects.
Choose only the BXD strains for the proof-of-concept example - this helped
bring out the fact that the traits file SHOULD NOT contain a strain column
for a strain that does not exist in the genotype file in consideration.
If the traits file has a strain column which does not exist in the genotype
file, then `rust-qtlreaper` fails with a panic, since, from what I can tell,
it tries to get a value from the genotype file for the non-existent strain,
which results to a `None` type. Subsequent attempts at running an operation
on the `None` type lead to the panic.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/heatmaps/heatmaps.py: document format of the traits file
To assist future developers, and development of the system, this commit
documents some of the hard-won knowledge about the operation of the system
to ease future development of the system.
The documentation, if good, might also help with future onboarding of new
developers to the system.
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* guix.scm: New package propagated-input.
* README.md: Mention that you require "guix-bioinformatics" package, because
of the addition of "gemma-wrapper".
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