X-Git-Url: https://git.hcoop.net/jackhill/guix/guix.git/blobdiff_plain/717e53fdc085e3a7b71b9f37da2358282289add4..166472e2c8535e5b5e19e34aeaa0f84cb978b4e3:/gnu/packages/bioinformatics.scm

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c49dec1b7e..172bb85791 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7729,13 +7729,13 @@ BLAST, KEGG, GenBank, MEDLINE and GO.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.58.0")
+    (version "1.58.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "0f0aa51h9x8n114zz6q6iw45d78i9wzl4ycbpiy0bdn23167pd84"))))
+                "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -7757,13 +7757,13 @@ also known as views, in a controlled vocabulary.")
 (define-public r-biocstyle
   (package
     (name "r-biocstyle")
-    (version "2.18.0")
+    (version "2.18.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocStyle" version))
               (sha256
                (base32
-                "1hfdvld0n9py45mxm05kbb0sq0s9p8yky3s6jb02gzhlxkk3q4fs"))))
+                "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp"))))
     (properties
      `((upstream-name . "BiocStyle")))
     (build-system r-build-system)
@@ -7913,13 +7913,13 @@ ID and species.  It is used by functions in the GenomeInfoDb package.")
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.26.0")
+    (version "1.26.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "1xfhz7gmccijy2z015w07lh04g0ijh7zi6k7q6m4lripgban93g9"))))
+                "092izc49maxjhf6m4b0qx21ad16dz7bmxy5pysp3vkyhdrfa2f7v"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
@@ -7980,8 +7980,6 @@ CAGE.")
                 "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
-    (inputs
-     `(("zlib" ,zlib)))
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
        ("r-biobase" ,r-biobase)
@@ -8260,8 +8258,6 @@ biological sequences or sets of sequences.")
              (substitute* "NAMESPACE"
                (("import\\(zlibbioc\\)") ""))
              #t)))))
-    (inputs
-     `(("zlib" ,zlib)))
     (propagated-inputs
      `(("r-biocgenerics" ,r-biocgenerics)
        ("r-biocparallel" ,r-biocparallel)
@@ -8659,7 +8655,7 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
 (define-public r-genomationdata
   (package
     (name "r-genomationdata")
-    (version "1.14.0")
+    (version "1.22.0")
     (source (origin
               (method url-fetch)
               ;; We cannot use bioconductor-uri here because this tarball is
@@ -8669,7 +8665,7 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
                                   "genomationData_" version ".tar.gz"))
               (sha256
                (base32
-                "10xyb8akjrhmak2i0mnv1agny2ipy364q9nlibyplpzc7vdb6bw7"))))
+                "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
     (build-system r-build-system)
     ;; As this package provides little more than large data files, it doesn't
     ;; make sense to build substitutes.
@@ -8794,9 +8790,8 @@ secondary structure and comparative analysis in R.")
     (arguments '(#:configure-flags '("--no-staged-install")))
     (propagated-inputs
      `(("curl" ,curl)
+       ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
        ("r-zlibbioc" ,r-zlibbioc)))
-    (inputs
-     `(("zlib" ,zlib)))
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("r-knitr" ,r-knitr)))
@@ -8827,8 +8822,6 @@ of other R packages who wish to make use of HTSlib.")
        ("r-rcpp" ,r-rcpp)
        ("r-rhtslib" ,r-rhtslib)
        ("r-zlibbioc" ,r-zlibbioc)))
-    (inputs
-     `(("zlib" ,zlib)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/bamsignals")
@@ -9076,21 +9069,57 @@ provided as a matrix which can be used as an offset for different expression
 of gene-level counts.")
     (license license:gpl2+)))
 
+(define-public r-rhdf5filters
+  (package
+    (name "r-rhdf5filters")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "rhdf5filters" version))
+       (sha256
+        (base32
+         "1jvnss44liapbc6hk93yg1gknv0ahd5x86dydqiwq9l65jd03psq"))))
+    (properties `((upstream-name . "rhdf5filters")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rhdf5lib" ,r-rhdf5lib)))
+    (inputs
+     `(("zlib" ,zlib)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/grimbough/rhdf5filters")
+    (synopsis "HDF5 compression filters")
+    (description
+     "This package provides a collection of compression filters for use with
+HDF5 datasets.")
+    (license license:bsd-2)))
+
 (define-public r-rhdf5
   (package
     (name "r-rhdf5")
-    (version "2.32.3")
+    (version "2.34.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rhdf5" version))
               (sha256
                (base32
-                "0fnx60dpf6s2qwq48lg98g18g8k7wgm66pw0kamlbb7l2hnwycvf"))))
+                "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi"))))
     (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-linking
+           (lambda _
+             (substitute* "src/Makevars"
+               ;; This is to avoid having a plain directory on the list of
+               ;; libraries to link.
+               (("\\(RHDF5_LIBS\\)" match)
+                (string-append match "/libhdf5.a")))
+             #t)))))
     (propagated-inputs
-     `(("r-rhdf5lib" ,r-rhdf5lib)))
-    (inputs
-     `(("zlib" ,zlib)))
+     `(("r-rhdf5filters" ,r-rhdf5filters)
+       ("r-rhdf5lib" ,r-rhdf5lib)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/rhdf5")
@@ -9578,8 +9607,6 @@ number detection tools.")
        ("r-zlibbioc" ,r-zlibbioc)))
     (native-inputs
      `(("r-knitr" ,r-knitr))) ; for vignettes
-    (inputs
-     `(("zlib" ,zlib)))
     (home-page "https://github.com/al2na/methylKit")
     (synopsis
      "DNA methylation analysis from high-throughput bisulfite sequencing results")
@@ -10182,14 +10209,14 @@ microarrays or GRanges for sequencing data.")
 (define-public r-keggrest
   (package
     (name "r-keggrest")
-    (version "1.30.0")
+    (version "1.30.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGREST" version))
        (sha256
         (base32
-         "0awg0hmxj25rpmqyf6jz6kbkswmimz3h352xx15xhkamwcxykng6"))))
+         "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s"))))
     (properties `((upstream-name . "KEGGREST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10525,16 +10552,26 @@ interval to data view, mismatch pileup, and several splicing summaries.")
 (define-public r-gqtlbase
   (package
     (name "r-gqtlbase")
-    (version "1.20.4")
+    (version "1.21.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gQTLBase" version))
        (sha256
         (base32
-         "1ly14vhhqxjpbxjypi6ppd37dycabdhf4ny4nsvp9969k418zv41"))))
+         "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
     (properties `((upstream-name . "gQTLBase")))
     (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; This is an upstream bug.
+         (add-after 'unpack 'fix-imports
+           (lambda _
+             (substitute* "NAMESPACE"
+               ((".*maxffmode.*") "")
+               (("importFrom\\(ff,.*") "import(ff)\n"))
+             #t)))))
     (propagated-inputs
      `(("r-batchjobs" ,r-batchjobs)
        ("r-bbmisc" ,r-bbmisc)
@@ -10695,14 +10732,14 @@ defining LD blocks.")
 (define-public r-gqtlstats
   (package
     (name "r-gqtlstats")
-    (version "1.20.0")
+    (version "1.21.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gQTLstats" version))
        (sha256
         (base32
-         "1jjqfpjp93nmxjn757j5mzcax96bzcqdd1gr3rsdxg7ap008l2w7"))))
+         "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
     (properties `((upstream-name . "gQTLstats")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10800,27 +10837,27 @@ with your data.")
 (define-public r-gwascat
   (package
     (name "r-gwascat")
-    (version "2.20.1")
+    (version "2.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gwascat" version))
        (sha256
         (base32
-         "1cq5cmdrf0a0arr841yvkh6d8drc15p7mif1afr215l1s3y2dwd4"))))
+         "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocfilecache" ,r-biocfilecache)
        ("r-biostrings" ,r-biostrings)
        ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicfeatures" ,r-genomicfeatures)
        ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
        ("r-iranges" ,r-iranges)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)))
+       ("r-readr" ,r-readr)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-snpstats" ,r-snpstats)
+       ("r-variantannotation" ,r-variantannotation)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://bioconductor.org/packages/gwascat")
@@ -10833,13 +10870,13 @@ EMBL-EBI GWAS catalog.")
 (define-public r-sushi
   (package
     (name "r-sushi")
-    (version "1.26.0")
+    (version "1.28.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Sushi" version))
               (sha256
                (base32
-                "17j3d5qjq5nbv99by5mq8rwr0jgh2jyyfn2nwxmwgzlmk3lgi1rb"))))
+                "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
     (properties `((upstream-name . "Sushi")))
     (build-system r-build-system)
     (propagated-inputs