build-system/gnu: Add 'bootstrap' phase.

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 439289e..b758c72 100644 (file)
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2074,7 +2074,7 @@ identify enrichments with functional annotations of the genome.")
 (define-public diamond
   (package
     (name "diamond")
-    (version "0.9.17")
+    (version "0.9.18")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2083,7 +2083,7 @@ identify enrichments with functional annotations of the genome.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1p3fd1ad7hg2w09w3sjk4pxqx0p0gaqys8ipg3f4adg77mn9m9yd"))))
+                "1vi2nddmy7knrv8gsprwqp6a40k63n3f2dfvx22ipjhrg9xir96f"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; no "check" target
@@ -4645,9 +4645,9 @@ distribution, coverage uniformity, strand specificity, etc.")
                        "Data2DB"
                        "PCL2Bin")))
            (modify-phases %standard-phases
-             (add-before 'configure 'bootstrap
+             (replace 'bootstrap
                (lambda _
-                 (zero? (system* "bash" "gen_auto"))))
+                 (invoke "bash" "gen_auto")))
              (add-after 'build 'build-additional-tools
                (lambda* (#:key make-flags #:allow-other-keys)
                  (every (lambda (dir)
@@ -6370,7 +6370,7 @@ SELECT or UPDATE queries to an end-point.")
 (define-public vsearch
   (package
     (name "vsearch")
-    (version "2.6.2")
+    (version "2.7.1")
     (source
      (origin
        (method url-fetch)
@@ -6380,7 +6380,7 @@ SELECT or UPDATE queries to an end-point.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "02khrgh8hm11cgww2f9mqc6886zqli9ss4pd4kfpqzd0d31vbzv5"))
+         "0jlzfgh79fzmb4g7sngzdjjsjyc37icvs1k7vmc2ksxglj6x5i7f"))
        (patches (search-patches "vsearch-unbundle-cityhash.patch"))
        (snippet
         '(begin
@@ -6672,27 +6672,28 @@ also known as views, in a controlled vocabulary.")
 
 (define-public r-bookdown
   (package
-  (name "r-bookdown")
-  (version "0.6")
-  (source (origin
-            (method url-fetch)
-            (uri (cran-uri "bookdown" version))
-            (sha256
-             (base32
-              "1pxxln42kvzl38fjprg6hcnyh1kij75fpj70vwp5hp5il813aszc"))))
-  (build-system r-build-system)
-  (propagated-inputs
-   `(("r-htmltools" ,r-htmltools)
-     ("r-knitr" ,r-knitr)
-     ("r-rmarkdown" ,r-rmarkdown)
-     ("r-yaml" ,r-yaml)
-     ("r-xfun" ,r-xfun)
-     ("ghc-pandoc" ,ghc-pandoc)))
-  (home-page "https://github.com/rstudio/bookdown")
-  (synopsis "Authoring books and technical documents with R markdown")
-  (description "This package provides output formats and utilities for
+    (name "r-bookdown")
+    (version "0.7")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "bookdown" version))
+              (sha256
+               (base32
+                "1b3fw1f41zph5yw3kynb47aijq53vhaa6mnnvxly72zamyzdf95q"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-htmltools" ,r-htmltools)
+       ("r-knitr" ,r-knitr)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-tinytex" ,r-tinytex)
+       ("r-yaml" ,r-yaml)
+       ("r-xfun" ,r-xfun)
+       ("ghc-pandoc" ,ghc-pandoc)))
+    (home-page "https://github.com/rstudio/bookdown")
+    (synopsis "Authoring books and technical documents with R markdown")
+    (description "This package provides output formats and utilities for
 authoring books and technical documents with R Markdown.")
-  (license license:gpl3)))
+    (license license:gpl3)))
 
 (define-public r-biocstyle
   (package
@@ -6768,14 +6769,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
 (define-public r-getopt
   (package
     (name "r-getopt")
-    (version "1.20.1")
+    (version "1.20.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "getopt" version))
        (sha256
         (base32
-         "0m463mcvixh54i3ng42n0vxmdlf97dgbfs2sf9wnjm782ddw68hm"))))
+         "13p35lbpy7i578752fa71sbfvcsqw5qfa9p6kf8b5m3c5p9i4v1x"))))
     (build-system r-build-system)
     (home-page "https://github.com/trevorld/getopt")
     (synopsis "Command-line option processor for R")
@@ -7088,13 +7089,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.30.1")
+    (version "1.30.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "1wnvvhj8yjsx242y6kfr5vs8kzisa96rxl1rgnnychrrvnvnh3i1"))))
+                "0c3r155603vb4zjs3adqa72770bh8karc11y8gl62l1m24jrkbnj"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -8110,7 +8111,7 @@ throughput genetic sequencing data sets using regression methods.")
 (define-public r-qtl
  (package
   (name "r-qtl")
-  (version "1.41-6")
+  (version "1.42-8")
   (source
    (origin
     (method url-fetch)
@@ -8118,7 +8119,7 @@ throughput genetic sequencing data sets using regression methods.")
                         version ".tar.gz"))
     (sha256
      (base32
-      "067az4v432zxp6lxck8d7vlh9w4r13r0mvw5zsglyaqwsh3d9sad"))))
+      "1l528dwvfpdlr05imrrm4rq32axp6hld9nqm6mm43kn5n7z2f5k6"))))
   (build-system r-build-system)
   (home-page "http://rqtl.org/")
   (synopsis "R package for analyzing QTL experiments in genetics")
@@ -8818,18 +8819,17 @@ replacement for strverscmp.")
 (define-public multiqc
   (package
     (name "multiqc")
-    (version "1.3")
+    (version "1.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "multiqc" version))
        (sha256
         (base32
-         "0fx1sx53znbgzfhbbiyd8j6cg5llpcsl5q5c45jy2c81d12piqfd"))))
+         "0ihx4rzmsfphv4byn05qv6f1y95g2dxs6viwziipl4wjk96acgm8"))))
     (build-system python-build-system)
     (propagated-inputs
-     `(("python-enum34" ,python-enum34)
-       ("python-jinja2" ,python-jinja2)
+     `(("python-jinja2" ,python-jinja2)
        ("python-simplejson" ,python-simplejson)
        ("python-pyyaml" ,python-pyyaml)
        ("python-click" ,python-click)
@@ -9394,13 +9394,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "2.2.0")
+    (version "2.2.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "1yarzhbylkfk4vwp7f8710zpdglkfww2db3hmq69hjllgg80ykmw"))
+                "1sr82nf38hq07avrfn8vlrzjq7dfm4pcr8l1nh6mnglcql2bk9z2"))
               ;; Delete pre-built jar.
               (snippet
                '(begin (delete-file "inst/java/ModularityOptimizer.jar")
@@ -9448,8 +9448,8 @@ Main-Class: ModularityOptimizer\n")))
        ("r-lars" ,r-lars)
        ("r-mass" ,r-mass)
        ("r-matrix" ,r-matrix)
+       ("r-metap" ,r-metap)
        ("r-mixtools" ,r-mixtools)
-       ("r-nmf" ,r-nmf)
        ("r-pbapply" ,r-pbapply)
        ("r-plotly" ,r-plotly)
        ("r-ranger" ,r-ranger)
@@ -9810,14 +9810,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-    (version "2.2.1")
+    (version "2.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ensembldb" version))
        (sha256
         (base32
-         "1vk6j0r5cczxmwbfzzkgayna66rxkfa3q2jikz649qvdiybhls40"))))
+         "1yngndkf3588z91z0a2fvkg423p26ajm6xv1p27x0l9mzhhaqq3k"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -9979,14 +9979,14 @@ interval to data view, mismatch pileup, and several splicing summaries.")
 (define-public r-gprofiler
   (package
     (name "r-gprofiler")
-    (version "0.6.1")
+    (version "0.6.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gProfileR" version))
        (sha256
         (base32
-         "1qix15d0wa9nspdclcawml94mng4qmr2jciv7d24py315wfsvv8p"))))
+         "1cka02zbz1rbppm782qpxk1xn9qxbrv2gp5rgf970j906hxm2y0b"))))
     (properties `((upstream-name . "gProfileR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10218,14 +10218,14 @@ family of feature/genome hypotheses.")
 (define-public r-gviz
   (package
     (name "r-gviz")
-    (version "1.22.2")
+    (version "1.22.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Gviz" version))
        (sha256
         (base32
-         "173n99mc95sij2vb8n3xd016x7mxhjs961q3l29xkg1lrnnm2sva"))))
+         "1grjzrjpzkw572pbvpsvdnfkfgwybl0cnjd7nnk2xdr26wnbsi9a"))))
     (properties `((upstream-name . "Gviz")))
     (build-system r-build-system)
     (propagated-inputs
@@ -10544,13 +10544,13 @@ libraries.")
 (define-public r-scater
   (package
     (name "r-scater")
-    (version "1.6.2")
+    (version "1.6.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scater" version))
               (sha256
                (base32
-                "0fp68n0xnbf90wrprqawsbilg9x7v2scp0dxb3936g20025csrdd"))))
+                "0q3s96gf8saa1dq2fvmpl0jyj7bx3wrdfck3hanb8pxkcir2p7dn"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-beachmat" ,r-beachmat)
@@ -10627,6 +10627,67 @@ cell-specific biases, assignment of cell cycle phase, and detection of highly
 variable and significantly correlated genes.")
     (license license:gpl3)))
 
+(define-public r-delayedmatrixstats
+  (package
+    (name "r-delayedmatrixstats")
+    (version "1.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "DelayedMatrixStats" version))
+       (sha256
+        (base32
+         "1cxjbjdq9hg9cm95rci0al7a4pk2h73ym276ahw9q4977zbg6381"))))
+    (properties
+     `((upstream-name . "DelayedMatrixStats")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-delayedarray" ,r-delayedarray)
+       ("r-iranges" ,r-iranges)
+       ("r-matrix" ,r-matrix)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
+    (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
+    (description
+     "This package provides a port of the @code{matrixStats} API for use with
+@code{DelayedMatrix} objects from the @code{DelayedArray} package.  It
+contains high-performing functions operating on rows and columns of
+@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
+@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}.  Functions
+are optimized per data type and for subsetted calculations such that both
+memory usage and processing time is minimized.")
+    (license license:expat)))
+
+(define-public r-dropbead
+  (let ((commit "cf0be5ae5302684bd03e78ab65b142900bbbb840")
+        (revision "1"))
+    (package
+      (name "r-dropbead")
+      (version (string-append "0-" revision "." (string-take commit 7)))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/rajewsky-lab/dropbead.git")
+               (commit commit)))
+         (sha256
+          (base32
+           "1b2lphsc236s1rdzlijxg8yl1jnqpwcvj4x938r89rqpj93jb780"))))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-ggplot2" ,r-ggplot2)
+         ("r-rcolorbrewer" ,r-rcolorbrewer)
+         ("r-gridextra" ,r-gridextra)
+         ("r-gplots" ,r-gplots)
+         ("r-plyr" ,r-plyr)))
+      (home-page "https://github.com/rajewsky-lab/dropbead")
+      (synopsis "Basic exploration and analysis of Drop-seq data")
+      (description "This package offers a quick and straight-forward way to
+explore and perform basic analysis of single cell sequencing data coming from
+droplet sequencing.  It has been particularly tailored for Drop-seq.")
+      (license license:gpl3))))
+
 (define htslib-for-sambamba
   (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
     (package
@@ -10643,13 +10704,6 @@ variable and significantly correlated genes.")
          (sha256
           (base32
            "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9"))))
-      (arguments
-       (substitute-keyword-arguments (package-arguments htslib)
-         ((#:phases phases)
-          `(modify-phases  ,phases
-             (add-after 'unpack 'bootstrap
-               (lambda _
-                 (zero? (system* "autoreconf" "-vif"))))))))
       (native-inputs
        `(("autoconf" ,autoconf)
          ("automake" ,automake)
@@ -10942,10 +10996,7 @@ programs for inferring phylogenies (evolutionary trees).")
     (arguments
      `(;; FIXME: Some tests fail because they produce warnings, others fail
        ;; because the PYTHONPATH does not include the modeller's directory.
-       #:tests? #f
-       ;; Do not place libraries in an architecture-specific directory.
-       #:configure-flags
-       (list "-DCMAKE_INSTALL_LIBDIR=lib")))
+       #:tests? #f))
     (inputs
      `(("boost" ,boost)
        ("gsl" ,gsl)
@@ -11800,3 +11851,31 @@ use of lightweight alignments (accurate but fast-to-compute proxies for
 traditional read alignments) and massively-parallel stochastic collapsed
 variational inference.")
     (license license:gpl3+)))
+
+(define-public python-loompy
+  (package
+    (name "python-loompy")
+    (version "2.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "loompy" version))
+       (sha256
+        (base32
+         "1drgv8j1hxqzzpnfg272x9djb6j8qr798w1pc2x8ikmfgyd9gh51"))))
+    (build-system python-build-system)
+    ;; There are no tests
+    (arguments '(#:tests? #f))
+    (propagated-inputs
+     `(("python-h5py" ,python-h5py)
+       ("python-numpy" ,python-numpy)
+       ("python-scipy" ,python-scipy)
+       ("python-typing" ,python-typing)))
+    (home-page "https://github.com/linnarsson-lab/loompy")
+    (synopsis "Work with .loom files for single-cell RNA-seq data")
+    (description "The loom file format is an efficient format for very large
+omics datasets, consisting of a main matrix, optional additional layers, a
+variable number of row and column annotations.  Loom also supports sparse
+graphs.  This library makes it easy to work with @file{.loom} files for
+single-cell RNA-seq data.")
+    (license license:bsd-3)))