diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 39 |
1 files changed, 24 insertions, 15 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 34289501fc..a573ef682f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7367,13 +7367,13 @@ S4Vectors package itself.") (define-public r-iranges (package (name "r-iranges") - (version "2.18.2") + (version "2.18.3") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0dc35844c1mfj07hvy6yn4wag6qdggbgl9gjcg3wpkh9hkm60a5n")))) + "05rw2b2bwns443n7d6lf97zdv1jbqdii2nprhs6x852w73m2a2g3")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -7647,13 +7647,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.40.4") + (version "2.40.5") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0dj51qkxm7bh24b3bs1di7lic6zgi7g5gf9iqkqhrwkbm7sqvn0v")))) + "1kjvxnkpsx3j2hji3cg3ka2gv8a9mg117lzzxyqjb7qa4zw7dipx")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -7731,13 +7731,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.0.0") + (version "2.0.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "1nv5idyjk75mvl4np5sig0xa6qygm1ivj33k041ffyj19q8jf7ij")))) + "188k5g40lbli7dxr96hldyvg9r9hmlbh2fp0qs5nnd12b8zbf338")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -8283,14 +8283,14 @@ secondary structure and comparative analysis in R.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.16.1") + (version "1.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "178zbrm221rwhbjk7j2v9g5ra44k0xg7c5abhd810m3g7snma8k8")))) + "07qaqj2hypmrg40m3pci082bzar6wi10dh77r4a8x74dfppcwdzf")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, @@ -8407,6 +8407,13 @@ library implementing most of the pipeline's features.") (arguments `(#:phases (modify-phases %standard-phases + (add-before 'configure 'find-RCAS + ;; The configure script can't find non-1.3.x versions of RCAS because + ;; its R expression ‘1.10.1 >= 1.3.4’ evaluates to false. + (lambda _ + (substitute* "configure" + (("1\\.3\\.4") "0.0.0")) + #t)) (add-after 'install 'wrap-executable (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -9165,14 +9172,14 @@ proteomics packages.") (define-public r-mzr (package (name "r-mzr") - (version "2.18.0") + (version "2.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "0g5r6yk4gyz0xdwlmrcij4zv7apdgsgygr043095l33hard6nsl5")) + "1pr1pcrg3r3pccm5ag6l8ic6rpqbk9jnlb9mm7g4ak5jwrajbzjq")) (modules '((guix build utils))) (snippet '(begin @@ -9193,7 +9200,8 @@ proteomics packages.") -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) #t))))) (inputs - `(;; XXX Boost 1.69 will not work here. + `(;; Our default boost package won't work here, unfortunately, even with + ;; mzR version 2.18.1. ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources ("zlib" ,zlib))) (propagated-inputs @@ -9446,13 +9454,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "3.1.0") + (version "3.1.1") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "0icxndnnkkmmr9hhd01dv3w8pih7x9r0rlp3fq9pk3qajp9gmlyq")))) + "084lr2fjdksshsmv1ww82bgn3a9mml7kswsidjrs89snabgvn360")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -9465,6 +9473,7 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-ggridges" ,r-ggridges) + ("r-httr" ,r-httr) ("r-ica" ,r-ica) ("r-igraph" ,r-igraph) ("r-irlba" ,r-irlba) @@ -10267,14 +10276,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.28.1") + (version "1.28.3") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0chsb3ijwd8zh588s1vqgfassn2rzax5rhqrhl0ini6pi4ilchp2")))) + "0347r1ly0vzpilflzbyzsjdf4cday294lw3fxzx61clblrmws1ki")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs |