diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 1 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 13 | ||||
| -rw-r--r-- | gn/packages/r-shiny.scm | 47 |
3 files changed, 55 insertions, 6 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index ef30d23..02c979d 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -4594,6 +4594,7 @@ interface to the basic htslib. It can be easily included in a C++ program for scripting high-performance genomic analyses.") (license license:asl2.0))) + (define-public r-stitch (package (name "r-stitch") diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 349e1c3..f362c4e 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -116,7 +116,7 @@ ((#:tests? _ #f) #f))))) (define-public genenetwork3 - (let ((commit "4e9bfd1b134eae4de365d1c2b22a97dd676b45b9") + (let ((commit "c0c6cc4110a5fe5c11b3a6994151ac9e807417dc") (revision "5")) (package (name "genenetwork3") @@ -130,7 +130,7 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0xn8gfsjd41afpgkp1hjyfvx241q47b8ri200fc7kx1kb8vyyhm6")))) + "1mhan38w68x5f9q285f4difd68bqz1ibvb54lfvx174i7wpn3gy7")))) (inputs (list python-click)) (native-inputs @@ -224,7 +224,7 @@ storage.") (license license:bsd-3))) (define-public genenetwork2 - (let ((commit "e1b1e2e14356e67d54e98d4e83b57158f17dc3c0") + (let ((commit "3385af399fd65eae3ff3c5216c412ae882b6f548") (revision "4")) (package (name "genenetwork2") @@ -237,7 +237,7 @@ storage.") (file-name (string-append name "-" version)) (sha256 (base32 - "0x92n27inbqgrx6fjaada0a8nf97a9jvrggncfqm0zih461nphr6")))) + "0skbjlsk9yniaz1yyldhssq0ax81g228xys0z65appacbsa8kczp")))) (native-inputs (list graphviz)) (propagated-inputs @@ -527,7 +527,7 @@ storage.") (license license:agpl3+)))) (define-public gn-auth - (let ((commit "8ff5d551633177d5ff07544348b2e04c4de5654e") + (let ((commit "aed581372c7c6b04023c85ce81943555cac363e6") (revision "01")) (package (name "gn-auth") @@ -538,10 +538,11 @@ storage.") (uri (git-reference (url "https://git.genenetwork.org/gn-auth") (commit commit))) + (file-name (git-file-name name version)) (hash (content-hash (base32 - "1pjcbrvmqipbni65ffq808gxzh2ywdwi28pm3gfqwq1z1jf627sx"))))) + "138nb087h71xda87skl3cw7q8vcfc24yq7k08xv0kyjpcmwybsvq"))))) (build-system python-build-system) (arguments (list diff --git a/gn/packages/r-shiny.scm b/gn/packages/r-shiny.scm index 898ee72..c2e61a6 100644 --- a/gn/packages/r-shiny.scm +++ b/gn/packages/r-shiny.scm @@ -1,6 +1,10 @@ (define-module (gn packages r-shiny) #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix download) + #:use-module (guix build-system r) #:use-module (guix packages) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (gnu packages bioconductor) #:use-module (gnu packages cran) #:use-module (gnu packages javascript)) @@ -12,3 +16,46 @@ (define-public js-es5-shim-2 (deprecated-package "js-es5-shim" js-es5-shim)) + + +(define-public r-runit + (package + (name "r-runit") + (version "0.4.33") + (source + (origin + (method url-fetch) + (uri (cran-uri "RUnit" version)) + (sha256 + (base32 "0pybwvd57vf71vvlxdrynw5n6s5gnbqnwvq0qpd395ggqypwb95j")))) + (properties `((upstream-name . "RUnit"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/package=RUnit") + (synopsis "R Unit Test Framework") + (description + "R functions implementing a standard Unit Testing framework, with additional code +inspection and report generation tools.") + (license license:gpl2))) + +(define-public r-org-rn-eg-db ; used by jumpshiny service + (package + (name "r-org-rn-eg-db") + (version "3.20.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "org.Rn.eg.db" version 'annotation)) + (sha256 + (base32 + "009c22ry5nnklzdc5dywnf8lq41cj3141yr5vw1kgifys6lanj01")))) + (properties + `((upstream-name . "org.Rn.eg.db"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi)) + (native-inputs (list r-runit)) + (home-page "https://www.bioconductor.org/packages/org.Rn.eg.db/") + (synopsis "Genome wide annotation for Rat") + (description + "This package provides mappings from Entrez gene identifiers to various +annotations for the genome of the rat.") + (license license:artistic2.0))) |