gnu: jamm: Update to 1.0.7.6.

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c71adbe..753b7fd 100644 (file)
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
@@ -2744,7 +2744,7 @@ quantitative phenotypes.")
 (define-public edirect
   (package
     (name "edirect")
-    (version "12.1.20190819")
+    (version "12.1.20190829")
     (source (origin
               (method url-fetch)
               (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect"
@@ -2752,7 +2752,7 @@ quantitative phenotypes.")
                                   "/edirect-" version ".tar.gz"))
               (sha256
                (base32
-                "1i9s9mppcfqd60pfywpm8vdyz5vpnyslw22nd7dv0bhykrdnkz9g"))))
+                "1xb330z28dgp7slrvp8r7rgncsasv9lpcpqim571yg728dq7xdik"))))
     (build-system perl-build-system)
     (arguments
      `(#:phases
@@ -4733,7 +4733,17 @@ interrupted by stop codons.  OrfM finds and prints these ORFs.")
                (base32
                 "1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i"))))
     (build-system python-build-system)
-    (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7
+    (arguments
+     `(#:python ,python-2               ;pbcore < 2.0 requires Python 2.7
+       #:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'remove-sphinx-dependency
+                    (lambda _
+                      ;; Sphinx is only required for documentation tests, which
+                      ;; we do not run; furthermore it depends on python2-sphinx
+                      ;; which is no longer maintained.
+                      (substitute* "requirements-dev.txt"
+                        (("^sphinx") ""))
+                      #t)))))
     (propagated-inputs
      `(("python-cython" ,python2-cython)
        ("python-numpy" ,python2-numpy)
@@ -4741,7 +4751,6 @@ interrupted by stop codons.  OrfM finds and prints these ORFs.")
        ("python-h5py" ,python2-h5py)))
     (native-inputs
      `(("python-nose" ,python2-nose)
-       ("python-sphinx" ,python2-sphinx)
        ("python-pyxb" ,python2-pyxb)))
     (home-page "https://pacificbiosciences.github.io/pbcore/")
     (synopsis "Library for reading and writing PacBio data files")
@@ -6926,14 +6935,14 @@ testing and other simple calculations.")
 (define-public r-shortread
   (package
     (name "r-shortread")
-    (version "1.44.1")
+    (version "1.44.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ShortRead" version))
        (sha256
         (base32
-         "1dh3q83hmi4l72vpif6dn51dzbi9ljrjgkq2zxg4sqy2jxv4vwza"))))
+         "0ykyrj4g6vc67d5s46sp4659qvar2iavflzhggm79w4p50hxia4s"))))
     (properties `((upstream-name . "ShortRead")))
     (build-system r-build-system)
     (inputs
@@ -7349,13 +7358,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.24.2")
+    (version "0.24.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "1s1h00k2ki7sd0hz4l8n41xr6ixszag7lm0ryrbb08idgcy16ipn"))))
+                "01f7dms4kw9ajwqlvh5s47riv748xrrs41na03byhjvn4fbdc44y"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -7523,13 +7532,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.42.0")
+    (version "3.42.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "0cfynv6qbnar5rl7vjh5lvddd381g9wqx1zd6a7l130hf59mwswn"))))
+                "1nd01r7rd7jb5qz84vbgfnyrmgm9wiq7fsdji68537kjgvrzmm9z"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -7742,13 +7751,13 @@ biological sequences or sets of sequences.")
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "2.2.1")
+    (version "2.2.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "0hpdc88prpq1gcja89n5s1ndcg81523qrkbkm9gbhm7rm8wmi8cl"))))
+                "1larx1a9cngmcsm2n7yyxrlnk69zi8m9dp3b90jva0ynspyi76v7"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)
@@ -7930,13 +7939,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.38.0")
+    (version "1.38.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "0xd9rlsicycbanbcfhc97cj8b8vk94g7lkbmhk37w1511bq35wz5"))))
+                "0dd226kgks50jdx5w35f3wmg95hy8aibi4kcn8p5kmqp5i8j580b"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -8227,7 +8236,7 @@ throughput genetic sequencing data sets using regression methods.")
 (define-public r-qtl
  (package
   (name "r-qtl")
-  (version "1.44-9")
+  (version "1.45-11")
   (source
    (origin
     (method url-fetch)
@@ -8235,7 +8244,7 @@ throughput genetic sequencing data sets using regression methods.")
                         version ".tar.gz"))
     (sha256
      (base32
-      "03lmvydln8b7666b6w46qbryhf83vsd11d4y2v95rfgvqgq66l1i"))))
+      "1d6qgj602fm6zia3djl4hmca0ri4v57ffp3g93p2yc3cabx2hq90"))))
   (build-system r-build-system)
   (home-page "https://rqtl.org/")
   (synopsis "R package for analyzing QTL experiments in genetics")
@@ -8323,14 +8332,14 @@ secondary structure and comparative analysis in R.")
 (define-public r-rhtslib
   (package
     (name "r-rhtslib")
-    (version "1.18.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rhtslib" version))
        (sha256
         (base32
-         "04inkq44lxwymqv51mxgaphasqjcdc9rl5p58imnrdm0kszs8prm"))))
+         "0gkbrmrcg55c9s5166ifljlx0v25rv4ijdyp4wf4c292xd6chy2l"))))
     (properties `((upstream-name . "Rhtslib")))
     (build-system r-build-system)
     ;; Without this a temporary directory ends up in the Rhtslib.so binary,
@@ -9495,13 +9504,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "3.1.2")
+    (version "3.1.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "0m1qi39snbmkkv1p07bzg1r7snc9x6a1y0dghvpk1nzgcfpmnsj4"))))
+                "0962mfgqk1di3wy1j0xdkvnw0q5m3q4xzd67d1l6dijlqiz8nfal"))))
     (properties `((upstream-name . "Seurat")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9540,7 +9549,6 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
        ("r-rtsne" ,r-rtsne)
        ("r-scales" ,r-scales)
        ("r-sctransform" ,r-sctransform)
-       ("r-sdmtools" ,r-sdmtools)
        ("r-tsne" ,r-tsne)
        ("r-uwot" ,r-uwot)))
     (home-page "http://www.satijalab.org/seurat")
@@ -10317,14 +10325,14 @@ family of feature/genome hypotheses.")
 (define-public r-gviz
   (package
     (name "r-gviz")
-    (version "1.30.0")
+    (version "1.30.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Gviz" version))
        (sha256
         (base32
-         "1p7n4yc77272rd8ybsim3rcg6kf6wmc95pwwav40b754imxn263z"))))
+         "0c9i26h5czm60n1bxzmdxxpywcj0sig6wcj913pb41mr83bbgra3"))))
     (properties `((upstream-name . "Gviz")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10469,14 +10477,14 @@ provided.")
 (define-public r-hdf5array
   (package
     (name "r-hdf5array")
-    (version "1.14.1")
+    (version "1.14.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "HDF5Array" version))
        (sha256
         (base32
-         "04hd02zd5jix5p2zg10asmwjg1fynqgmclbhbmk7fb6arx5hm11f"))))
+         "0mbx9rsr2571k4k4hmx3dr49rhqb31dhwy2r2bkrd4dbhvriqgld"))))
     (properties `((upstream-name . "HDF5Array")))
     (build-system r-build-system)
     (inputs
@@ -10666,14 +10674,14 @@ quality control.")
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.14.5")
+    (version "1.14.6")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "0ydy6gvpgpvrs4ryk1qvmmxp6cpaizs294jwg42jawxndkds1l3y"))))
+         "1y8wlgk5zbv7c7gcp0ahfpbh9lifab7y3zwf0093fzaw7vr1y6cr"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beachmat" ,r-beachmat)
@@ -12937,14 +12945,14 @@ analyses in addition to large-scale sequence-level searches.")
 (define-public r-diversitree
   (package
     (name "r-diversitree")
-    (version "0.9-11")
+    (version "0.9-13")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "diversitree" version))
         (sha256
          (base32
-          "1jqfjmmaigq581l4zxysmkhld0xv6izlbr1hihf9zplkix36majc"))))
+          "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -13874,7 +13882,7 @@ absolute GSEA.")
 (define-public jamm
   (package
     (name "jamm")
-    (version "1.0.7.5")
+    (version "1.0.7.6")
     (source
      (origin
        (method git-fetch)
@@ -13884,7 +13892,7 @@ absolute GSEA.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0ls889jcma1ch9h21jjhnkadgszgqj41842hhcjh6cg88f85qf3i"))))
+         "0bsa5mf9n9q5jz7mmacrra41l7r8rac5vgsn6wv1fb52ya58b970"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; there are none