diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 59 |
1 files changed, 55 insertions, 4 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 04ed769cd8..f5e7285193 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1482,7 +1482,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.8.5") + (version "0.8.7") (source (origin (method url-fetch) (uri (string-append @@ -1491,7 +1491,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "18zx8k3axnsrg016kikl8xs1ifnjmj36dk1sv3fq1jgpg9j9584b")))) + "15r7gcrqc4pv5d4kvv530zc3xnni92c74y63zrxzidriss7591yx")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target @@ -3815,10 +3815,61 @@ data in the form of VCF files.") ;; at https://vcftools.github.io/license.html (license license:lgpl3))) +(define-public r-vegan + (package + (name "r-vegan") + (version "2.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "vegan" version)) + (sha256 + (base32 + "10cygzkyg2m0y054ygivqxrkvqz792qsg6bmbdfzaqq37qv4wc7z")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'revert-test-deletion + ;; The distributed sources do not include tests with the CRAN + ;; package. Here we revert the commit + ;; `591d0e8ba1deaaf82445474ec6619c0b43db4e63' which deletes these + ;; tests. There are plans to not delete tests in future as + ;; documented at https://github.com/vegandevs/vegan/issues/181. + (lambda* (#:key inputs #:allow-other-keys) + (zero? + (system* "patch" "-R" "-p1" "-i" + (assoc-ref inputs "r-vegan-delete-tests-patch")))))))) + (native-inputs + `(("gfortran" ,gfortran) + ("r-knitr" ,r-knitr) + ("r-vegan-delete-tests-patch" + ,(origin + (method url-fetch) + (uri (string-append + "https://github.com/vegandevs/vegan/commit/" + "591d0e8ba1deaaf82445474ec6619c0b43db4e63.patch")) + (sha256 + (base32 + "0b1bi7y4jjdl3ph721vm9apm51dr2z9piwvhy4355sf2b4kyyj5a")))))) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-lattice" ,r-lattice) + ("r-mgcv" ,r-mgcv) + ("r-permute" ,r-permute))) + (home-page "https://cran.r-project.org/web/packages/vegan") + (synopsis "Functions for community ecology") + (description + "The vegan package provides tools for descriptive community ecology. It +has most basic functions of diversity analysis, community ordination and +dissimilarity analysis. Most of its multivariate tools can be used for other +data types as well.") + (license license:gpl2+))) + (define-public vsearch (package (name "vsearch") - (version "1.11.1") + (version "2.0.0") (source (origin (method url-fetch) @@ -3828,7 +3879,7 @@ data in the form of VCF files.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1pdvm3znjgq3zryy240yj9gc0bf1z31k6vf9jxrxgdgkvzgw85c7")) + "1sd57abgx077icqrbj36jq9q7pdpzc6dbics2pn1555kisq2jhfh")) (modules '((guix build utils))) (snippet '(begin |