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-rw-r--r--gn/packages/bioinformatics.scm90
1 files changed, 90 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 12595ab..6dde766 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -3096,3 +3096,93 @@ their chance of getting selected as minimizers.")
;; Meryl is mix bsd-3, expat and public-domain.
;; Rest of the code is public domain.
(license license:expat)))
+
+;; TODO: Regenerate or remove docs folder.
+(define-public python-pixy
+ (package
+ (name "python-pixy")
+ (version "1.2.6.beta1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ksamuk/pixy")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "16hl6hcf38fya18b1x75250z1shsysvpmc75vsp6wjqggajcfqc7"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ ;; "Test" based on test command in conda recipe.
+ (invoke "pixy" "--version")))))))
+ (propagated-inputs
+ (list python-multiprocess
+ python-numcodecs
+ python-numpy
+ python-pandas
+ python-scikit-allel
+ python-scipy))
+ (home-page "https://pixy.readthedocs.io/")
+ (synopsis
+ "Unbiased estimation of nucleotide diversity within and between populations")
+ (description "@command{pixy} is a command-line tool for painlessly
+estimating average nucleotide diversity within (π) and between (dxy) populations
+from a VCF. In particular, pixy facilitates the use of VCFs containing
+invariant (monomorphic) sites, which are essential for the correct computation
+of π and dxy in the face of missing data (i.e. always).")
+ (license license:expat)))
+
+(define-public python-scikit-allel
+ (package
+ (name "python-scikit-allel")
+ (version "1.3.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "scikit-allel" version))
+ (sha256
+ (base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "python" "setup.py" "build_ext" "--inplace")
+ (invoke "python" "-m" "pytest" "-v" "allel"
+ ;; AttributeError: 'Dataset' object has no attribute 'asstr'
+ ;; Perhaps need python-h5py@3?
+ "-k" (string-append
+ "not test_vcf_to_hdf5"
+ " and not test_vcf_to_hdf5_exclude"
+ " and not test_vcf_to_hdf5_rename"
+ " and not test_vcf_to_hdf5_group"
+ " and not test_vcf_to_hdf5_ann"))))))))
+ (propagated-inputs
+ (list python-dask
+ python-numpy))
+ (native-inputs
+ (list python-cython
+ ;; The following are all needed for the tests
+ htslib
+ python-h5py
+ python-hmmlearn
+ python-numexpr
+ python-pytest
+ python-scipy
+ python-setuptools-scm
+ python-zarr))
+ (home-page "https://github.com/cggh/scikit-allel")
+ (synopsis "Explore and analyze genetic variation data")
+ (description
+ "This package provides utilities for exploratory analysis of large scale
+genetic variation data.")
+ (license license:expat)))