gnu: dealii: Update to 8.5.0.

[jackhill/guix/guix.git] / gnu / packages / bioinformatics.scm

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4c21a21..c08297d 100644 (file)
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -48,6 +48,7 @@
   #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpio)
+  #:use-module (gnu packages cran)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages databases)
@@ -1636,7 +1637,7 @@ databases.")
     (build-system python-build-system)
     (arguments `(#:python ,python-2)) ; only Python 2 is supported
     (inputs
-     `(("htseq" ,htseq)
+     `(("htseq" ,python2-htseq)
        ("python-pybedtools" ,python2-pybedtools)
        ("python-cython" ,python2-cython)
        ("python-scikit-learn" ,python2-scikit-learn)
@@ -2981,22 +2982,22 @@ HMMs).")
 (define-public htseq
   (package
     (name "htseq")
-    (version "0.6.1")
+    (version "0.9.1")
     (source (origin
               (method url-fetch)
-              (uri (string-append
-                    "https://pypi.python.org/packages/source/H/HTSeq/HTSeq-"
-                    version ".tar.gz"))
+              (uri (pypi-uri "HTSeq" version))
               (sha256
                (base32
-                "1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv"))))
+                "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg"))))
     (build-system python-build-system)
-    (arguments `(#:python ,python-2)) ; only Python 2 is supported
+    (native-inputs
+     `(("python-cython" ,python-cython)))
     ;; Numpy needs to be propagated when htseq is used as a Python library.
     (propagated-inputs
-     `(("python-numpy" ,python2-numpy)))
+     `(("python-numpy" ,python-numpy)))
     (inputs
-     `(("python-pysam" ,python2-pysam)))
+     `(("python-pysam" ,python-pysam)
+       ("python-matplotlib" ,python-matplotlib)))
     (home-page "http://www-huber.embl.de/users/anders/HTSeq/")
     (synopsis "Analysing high-throughput sequencing data with Python")
     (description
@@ -3004,6 +3005,9 @@ HMMs).")
 from high-throughput sequencing assays.")
     (license license:gpl3+)))
 
+(define-public python2-htseq
+  (package-with-python2 htseq))
+
 (define-public java-htsjdk
   (package
     (name "java-htsjdk")
@@ -5752,14 +5756,14 @@ high-throughput sequencing experiments.")
 (define-public r-deseq2
   (package
     (name "r-deseq2")
-    (version "1.16.0")
+    (version "1.16.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DESeq2" version))
        (sha256
         (base32
-         "0m0apn3xi4kdkinsj4xkw5cwysicyjr6xxlxhpa4scyv589am1s5"))))
+         "01pvyljxkwazxl510v7h0971nx65iqd2bdkbdhw3xzind0n9pdvq"))))
     (properties `((upstream-name . "DESeq2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5789,14 +5793,14 @@ distribution.")
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.18.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "01kd86vvgpa4a5zivcy4g6z8rhcykasdskrz8yqsqz211sd1xsr3"))))
+         "1366qvykd9cpcvwgc5g9mm9adw9rxw6p4814dd6l5fyb0pwpmysx"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)
@@ -5867,14 +5871,14 @@ Enrichment Analysis} (GSEA).")
 (define-public r-category
   (package
     (name "r-category")
-    (version "2.42.0")
+    (version "2.42.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Category" version))
        (sha256
         (base32
-         "0swcmihyjg0fhaaydl9hm24aj9zffw3bibza9y6sqs6jaqd97f09"))))
+         "1w186nhc85bglcgmbcrsdbb8l6rph21pl5kdwjqwkp0jnr9z0ifn"))))
     (properties `((upstream-name . "Category")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6379,13 +6383,13 @@ also known as views, in a controlled vocabulary.")
 (define-public r-bookdown
   (package
   (name "r-bookdown")
-  (version "0.3")
+  (version "0.4")
   (source (origin
             (method url-fetch)
             (uri (cran-uri "bookdown" version))
             (sha256
              (base32
-              "0r9bchzg7im6psc3jphvshzbidc5bv5xaih1qg7b5518jy4iyvb9"))))
+              "1fp1k7hivrb7s2dwgrsqy9s7xg6pk9hczhrc149y1dwh901j6qvv"))))
   (build-system r-build-system)
   (propagated-inputs
    `(("r-htmltools" ,r-htmltools)
@@ -6401,13 +6405,13 @@ authoring books and technical documents with R Markdown.")
 (define-public r-biocstyle
   (package
    (name "r-biocstyle")
-   (version "2.4.0")
+   (version "2.4.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocStyle" version))
               (sha256
                (base32
-                "1n2c8rj920wmk3q2khmjfnhn5i4b3lmhx1whnghk0zk3jf88hvbi"))))
+                "0bmgmsfll923v573g0kyzlmjd7gly5jwgd8vkrcwvbam1gz75f2c"))))
     (properties
      `((upstream-name . "BiocStyle")))
     (build-system r-build-system)
@@ -6495,14 +6499,14 @@ support for default values, positional argument support, etc.")
 (define-public r-optparse
   (package
     (name "r-optparse")
-    (version "1.3.2")
+    (version "1.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "optparse" version))
        (sha256
         (base32
-         "1g8as89r91xxi5j5azsd6vrfrhg84mnfx2683j7pacdp8s33radw"))))
+         "1ff4wmsszrb3spwfp7ynfs8w11qpy1sdzfxm1wk8dqqvdwris7qb"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-getopt" ,r-getopt)))
@@ -6567,14 +6571,14 @@ S4Vectors package itself.")
 (define-public r-seqinr
   (package
     (name "r-seqinr")
-    (version "3.3-6")
+    (version "3.4-5")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "seqinr" version))
         (sha256
           (base32
-            "13d0qxm2244wgdl2dy2s8vnrnf5fx4n47if9gkb49dqx6c0sx8s2"))))
+            "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ade4" ,r-ade4)
@@ -7571,7 +7575,7 @@ Stephens (1990).")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "0479qx4bapgcp5chj10a63chk0s28x9cx1gamz3f5m3yd7jzwcf2"))))
+                "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
     (properties
      `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
     (build-system r-build-system)
@@ -7812,7 +7816,7 @@ throughput genetic sequencing data sets using regression methods.")
 (define-public r-qtl
  (package
   (name "r-qtl")
-  (version "1.40-8")
+  (version "1.41-6")
   (source
    (origin
     (method url-fetch)
@@ -7820,7 +7824,7 @@ throughput genetic sequencing data sets using regression methods.")
                         version ".tar.gz"))
     (sha256
      (base32
-      "05bj1x2ry0i7yqiydlswb3d2h4pxg70z8w1072az1mrv1m54k8sp"))))
+      "067az4v432zxp6lxck8d7vlh9w4r13r0mvw5zsglyaqwsh3d9sad"))))
   (build-system r-build-system)
   (home-page "http://rqtl.org/")
   (synopsis "R package for analyzing QTL experiments in genetics")
@@ -8062,14 +8066,14 @@ in SNV base substitution data.")
 (define-public r-wgcna
   (package
     (name "r-wgcna")
-    (version "1.51")
+    (version "1.60")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "WGCNA" version))
        (sha256
         (base32
-         "0hzvnhw76vwg8bl8x368f0c5szpwb8323bmrb3bir93i5bmfjsxx"))))
+         "16mxhwzhh5q48wmz1iba2r21cp0n0v8g11am4pi52iv6g0663ixl"))))
     (properties `((upstream-name . "WGCNA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8649,14 +8653,14 @@ unmodeled, or latent sources of noise.")
 (define-public r-seqminer
   (package
     (name "r-seqminer")
-    (version "5.9")
+    (version "6.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "seqminer" version))
        (sha256
         (base32
-         "0sfkxrc9gy5a8fadzyzfzh7l5grasm8cj6cd2nnpv85ws6mqr6qd"))))
+         "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l"))))
     (build-system r-build-system)
     (inputs
      `(("zlib" ,zlib)))