diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 90 |
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))) |