Merge branch 'master' into staging

1 files changed, 859 insertions, 79 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d3b137513c..820bd84d66 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1,12 +1,12 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2015, 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.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>
 ;;;
@@ -71,6 +71,7 @@
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages java)
+  #:use-module (gnu packages jemalloc)
   #:use-module (gnu packages ldc)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages logging)
@@ -2038,7 +2039,7 @@ with Python.")
     (version "2.5.1")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://github.com/fidelram/deepTools/"
+              (uri (string-append "https://github.com/deeptools/deepTools/"
                                   "archive/" version ".tar.gz"))
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
@@ -2057,7 +2058,7 @@ with Python.")
      `(("python-mock" ,python-mock)   ;for tests
        ("python-nose" ,python-nose)   ;for tests
        ("python-pytz" ,python-pytz))) ;for tests
-    (home-page "https://github.com/fidelram/deepTools")
+    (home-page "https://github.com/deeptools/deepTools")
     (synopsis "Tools for normalizing and visualizing deep-sequencing data")
     (description
      "DeepTools addresses the challenge of handling the large amounts of data
@@ -2073,7 +2074,7 @@ identify enrichments with functional annotations of the genome.")
 (define-public diamond
   (package
     (name "diamond")
-    (version "0.9.14")
+    (version "0.9.18")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2082,7 +2083,7 @@ identify enrichments with functional annotations of the genome.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "07li3chjdna0wjyh680j3bhwiqh1fbfq9dy9jxxs82mc0rw0m1yy"))))
+                "1vi2nddmy7knrv8gsprwqp6a40k63n3f2dfvx22ipjhrg9xir96f"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; no "check" target
@@ -3433,7 +3434,7 @@ sometimes better.  Khmer can also identify and fix problems with shotgun
 data.")
     ;; When building on i686, armhf and mips64el, we get the following error:
     ;; error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system
-    (supported-systems '("x86_64-linux"))
+    (supported-systems '("x86_64-linux" "aarch64-linux"))
     (license license:bsd-3)))
 
 (define-public kaiju
@@ -5562,6 +5563,11 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
        (modify-phases %standard-phases
          (add-after 'unpack 'enter-source-dir
            (lambda _ (chdir "source") #t))
+         (add-after 'enter-source-dir 'make-reproducible
+           (lambda _
+             (substitute* "Makefile"
+               (("(COMPILATION_TIME_PLACE=\")(.*)(\")" _ pre mid post)
+                (string-append pre "Built with Guix" post)))))
          (add-after 'enter-source-dir 'do-not-use-bundled-htslib
            (lambda _
              (substitute* "Makefile"
@@ -5843,14 +5849,14 @@ information as possible.")
 (define-public r-vegan
   (package
     (name "r-vegan")
-    (version "2.4-5")
+    (version "2.4-6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vegan" version))
        (sha256
         (base32
-         "0cyyvn3xsjn24w590jn6z4xajafv7yzvj6c51vqi9q6m8v5831ya"))))
+         "175mqr42mmxy98gpf3rky8alnkw3w1k90ggdw3cispl36841p76w"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -6364,7 +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)
@@ -6374,7 +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
@@ -6666,25 +6672,28 @@ also known as views, in a controlled vocabulary.")
 
 (define-public r-bookdown
   (package
-  (name "r-bookdown")
-  (version "0.5")
-  (source (origin
-            (method url-fetch)
-            (uri (cran-uri "bookdown" version))
-            (sha256
-             (base32
-              "0zm63kr4f4kja4qpwkzl119zzyciqj7ihajfqgfjpgb4dzaiycxp"))))
-  (build-system r-build-system)
-  (propagated-inputs
-   `(("r-htmltools" ,r-htmltools)
-     ("r-knitr" ,r-knitr)
-     ("r-rmarkdown" ,r-rmarkdown)
-     ("r-yaml" ,r-yaml)))
-  (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
@@ -6760,14 +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")
@@ -6959,13 +6968,13 @@ names in their natural, rather than lexicographic, order.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.20.2")
+    (version "3.20.8")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "0j5s3i33qmld9l7gs1rzpv601zxyqz711x8mq35hml088c8s99w9"))))
+                "0g7bj6w61blw3m22hw9rc01n554k9qkjizh7njr3j4shmhads58d"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
@@ -6987,13 +6996,13 @@ CAGE.")
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.24.2")
+    (version "1.24.5")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "19wgb2kcqy97pm3xgqc781id9fbmzp1hdwzkkhdzpvyf29w4n29j"))))
+                "07ywn3c4w83l3sr76d0z3b1nv9icgdh3phsjlc6cfx7i6nfmvxw2"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (inputs
@@ -7025,13 +7034,13 @@ coding changes and predict coding outcomes.")
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.34.4")
+    (version "3.34.8")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "1vcxf9jg8xngxg5kb9bp8rw5sghpnkpj320iq309m2fp41ahsk3f"))))
+                "0bmxsgz2yll83sd3wbxsrsfd35468igb0d8lldym0d0lqfz906bw"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
@@ -7080,13 +7089,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
-    (version "1.30.0")
+    (version "1.30.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicRanges" version))
               (sha256
                (base32
-                "10ra2sjn17h6gilm9iz0cygp9ijpgbirljlc4drwrnivnw9cmi2a"))))
+                "0c3r155603vb4zjs3adqa72770bh8karc11y8gl62l1m24jrkbnj"))))
     (properties
      `((upstream-name . "GenomicRanges")))
     (build-system r-build-system)
@@ -7158,13 +7167,13 @@ annotation data packages using SQLite data storage.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.34.1")
+    (version "2.34.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "0jzv8b86vpvavwnzi5xf7y18xmn72zkabkn2kclg1mgl847cq13k"))))
+                "1zlgs2zg0lmnk572p55n7m34nkxka8w10x8f2ndssjkffl2csy79"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -7316,13 +7325,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
 (define-public r-summarizedexperiment
   (package
     (name "r-summarizedexperiment")
-    (version "1.8.0")
+    (version "1.8.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "SummarizedExperiment" version))
               (sha256
                (base32
-                "1011r8l0k8420j31bmh4xdcp6ka5bzf4bqhip84v5b6alpkcbvmf"))))
+                "19vlwnby83fqjrilsxvnvgz0gvby7mrxvlmx18nb3p1w591ddfjh"))))
     (properties
      `((upstream-name . "SummarizedExperiment")))
     (build-system r-build-system)
@@ -7380,13 +7389,13 @@ alignments.")
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.38.2")
+    (version "1.38.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "1sjn3976f1sqvrq6jq2hgc60ffxgfr3jlklaxfrk3xad5cv2kr2d"))))
+                "1khzfczm35k5lq9h0jlqrq01192spzjyh8s6is89spj006flwn4k"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
@@ -7425,13 +7434,13 @@ as well as query and modify the browser state, such as the current viewport.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.30.0")
+    (version "1.30.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "1khjvq1ffhqavkwf8n7bilknci60lxbg52icrcf2vnb9k8rlpghs"))))
+                "010vn8hlwbnw12pd1d8pv6m12yp3xwx557gba5rbjq9p4qypnn3z"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
@@ -7651,13 +7660,13 @@ reference point and sorted by a user defined feature.")
 (define-public r-genomation
   (package
     (name "r-genomation")
-    (version "1.10.0")
+    (version "1.11.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "genomation" version))
               (sha256
                (base32
-                "1ddd8c9w1f1i1ga9rpbwiic8rsaws1chdxx4j38bpyaiy4zhz1ca"))))
+                "1d2g1v6xhrf3gm86pv8ln22df5g6v6k6i4i39v4j82zn4apany6v"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biostrings" ,r-biostrings)
@@ -8102,7 +8111,7 @@ throughput genetic sequencing data sets using regression methods.")
 (define-public r-qtl
  (package
   (name "r-qtl")
-  (version "1.41-6")
+  (version "1.42-7")
   (source
    (origin
     (method url-fetch)
@@ -8110,7 +8119,7 @@ throughput genetic sequencing data sets using regression methods.")
                         version ".tar.gz"))
     (sha256
      (base32
-      "067az4v432zxp6lxck8d7vlh9w4r13r0mvw5zsglyaqwsh3d9sad"))))
+      "0hxij8v4my5x4pf5fn5327g7m3n7vjkbzrl580vcmp81n3n3nmrx"))))
   (build-system r-build-system)
   (home-page "http://rqtl.org/")
   (synopsis "R package for analyzing QTL experiments in genetics")
@@ -8356,14 +8365,14 @@ in SNV base substitution data.")
 (define-public r-wgcna
   (package
     (name "r-wgcna")
-    (version "1.61")
+    (version "1.62")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "WGCNA" version))
        (sha256
         (base32
-         "1vrc2k33a196hrrl7k0z534fp96vv0shmigcr65ny1q0v6lq0h6i"))))
+         "0c52rp09gqphz6g5x9jzkdcsyvfrknq0dkq9saslgy8q8ap974vx"))))
     (properties `((upstream-name . "WGCNA")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8461,14 +8470,14 @@ factors bound at the specific regions.")
 (define-public r-gkmsvm
   (package
     (name "r-gkmsvm")
-    (version "0.71.0")
+    (version "0.79.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gkmSVM" version))
        (sha256
         (base32
-         "1zpxgxmf2nd5j5wn00ps6kfxr8wxh7d1swr1rr4spq7sj5z5z0k0"))))
+         "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
     (properties `((upstream-name . "gkmSVM")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8810,18 +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)
@@ -8936,13 +8944,13 @@ number detection tools.")
 (define-public r-methylkit
   (package
     (name "r-methylkit")
-    (version "1.4.0")
+    (version "1.4.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "methylKit" version))
               (sha256
                (base32
-                "0h53w2mrjrg2n0ndi12k9j6cwclgwcgpy25nz7nyj971aisw02xn"))))
+                "1k0nfn9318sgwm4z963bhnbp4c3zv85v3f9886vc5hgaisr0yvai"))))
     (properties `((upstream-name . "methylKit")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9306,14 +9314,14 @@ structure (pcaRes) to provide a common interface to the PCA results.")
 (define-public r-msnbase
   (package
     (name "r-msnbase")
-    (version "2.4.0")
+    (version "2.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MSnbase" version))
        (sha256
         (base32
-         "0dqfimljhrx3gac8d1k72gppx27lz8yckyb12v4604nbviw7xd3r"))))
+         "1ig64bf881p118dwqfr0ry41m7yhnyv165smv8fdwfv7sb6sagif"))))
     (properties `((upstream-name . "MSnbase")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9386,13 +9394,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "2.1.0")
+    (version "2.2.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "1hqaq6bciikrsyw157w8fn4jw885air7xbkxrmism93rp4qx483x"))
+                "1sr82nf38hq07avrfn8vlrzjq7dfm4pcr8l1nh6mnglcql2bk9z2"))
               ;; Delete pre-built jar.
               (snippet
                '(begin (delete-file "inst/java/ModularityOptimizer.jar")
@@ -9429,8 +9437,8 @@ Main-Class: ModularityOptimizer\n")))
        ("r-fnn" ,r-fnn)
        ("r-fpc" ,r-fpc)
        ("r-gdata" ,r-gdata)
-       ("r-ggjoy" ,r-ggjoy)
        ("r-ggplot2" ,r-ggplot2)
+       ("r-ggridges" ,r-ggridges)
        ("r-gplots" ,r-gplots)
        ("r-gridextra" ,r-gridextra)
        ("r-hmisc" ,r-hmisc)
@@ -9440,13 +9448,14 @@ 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)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-rcpp" ,r-rcpp)
+       ("r-rcppeigen" ,r-rcppeigen)
        ("r-rcppprogress" ,r-rcppprogress)
        ("r-reshape2" ,r-reshape2)
        ("r-rocr" ,r-rocr)
@@ -9656,14 +9665,14 @@ microarrays or GRanges for sequencing data.")
 (define-public r-keggrest
   (package
     (name "r-keggrest")
-    (version "1.18.0")
+    (version "1.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "KEGGREST" version))
        (sha256
         (base32
-         "1i3i88lj57wvpgjf75a23msgfsjv8pr2b4j1faga276p4fsblkhj"))))
+         "02gwmm79djj55a90dzc80hlgwc6bafl7xd7fnx2q59pk945k3z9c"))))
     (properties `((upstream-name . "KEGGREST")))
     (build-system r-build-system)
     (propagated-inputs
@@ -9680,14 +9689,14 @@ microarrays or GRanges for sequencing data.")
 (define-public r-gage
   (package
     (name "r-gage")
-    (version "2.28.0")
+    (version "2.28.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gage" version))
        (sha256
         (base32
-         "1r14p88q3y736pkqm4pdimf1izy1xy3xgivmj3cr4dv65kjny1zk"))))
+         "0h0mlhns9j7cpfksvdlvx9jb7szm3r1dwqb3s4s8p8hmkb9byyii"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -9801,14 +9810,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-    (version "2.2.0")
+    (version "2.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ensembldb" version))
        (sha256
         (base32
-         "1w0lca3ws5j770bmls91cn93lznvv2pc8s42nybdzz3vdxjvb4m1"))))
+         "1yngndkf3588z91z0a2fvkg423p26ajm6xv1p27x0l9mzhhaqq3k"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -9970,14 +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
@@ -10209,14 +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
@@ -10396,6 +10405,289 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
     ;; Any version of the LGPL.
     (license license:lgpl3+)))
 
+(define-public r-hdf5array
+  (package
+    (name "r-hdf5array")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "HDF5Array" version))
+       (sha256
+        (base32
+         "0kcdza41saqv6vlpvqd841awbiwkg84lh0plx6c7fmfgbqv7a0jh"))))
+    (properties `((upstream-name . "HDF5Array")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-delayedarray" ,r-delayedarray)
+       ("r-iranges" ,r-iranges)
+       ("r-rhdf5" ,r-rhdf5)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/HDF5Array")
+    (synopsis "HDF5 back end for DelayedArray objects")
+    (description "This package provides an array-like container for convenient
+access and manipulation of HDF5 datasets.  It supports delayed operations and
+block processing.")
+    (license license:artistic2.0)))
+
+(define-public r-rhdf5lib
+  (package
+    (name "r-rhdf5lib")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Rhdf5lib" version))
+       (sha256
+        (base32
+         "0kkc4rprjbqn2wvbx4d49kk9l91vihccxbl4843qr1wqk6v33r1w"))))
+    (properties `((upstream-name . "Rhdf5lib")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'do-not-use-bundled-hdf5
+           (lambda* (#:key inputs #:allow-other-keys)
+             (for-each delete-file '("configure" "configure.ac"))
+             ;; Do not make other packages link with the proprietary libsz.
+             (substitute* "R/zzz.R"
+               (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a'")
+                "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a'")
+               (("'%s/libhdf5.a %s/libsz.a'")
+                "'%s/libhdf5.a %s/libhdf5.a'"))
+             (with-directory-excursion "src"
+               (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
+               (rename-file (string-append "hdf5-" ,(package-version hdf5))
+                            "hdf5")
+               (rename-file "Makevars.in" "Makevars")
+               (substitute* "Makevars"
+                 (("HDF5_CXX_LIB=.*")
+                  (string-append "HDF5_CXX_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
+                 (("HDF5_LIB=.*")
+                  (string-append "HDF5_LIB="
+                                 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
+                 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
+                 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
+                 ;; szip is non-free software
+                 (("cp \\$\\{SZIP_LIB\\}.*") "")
+                 (("PKG_LIBS = \\$\\{HDF5_LIB\\} \\$\\{SZIP_LIB\\}")
+                  "PKG_LIBS = ${HDF5_LIB}\n")))
+             #t)))))
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("hdf5" ,hdf5)))
+    (native-inputs
+     `(("hdf5-source" ,(package-source hdf5))))
+    (home-page "https://bioconductor.org/packages/Rhdf5lib")
+    (synopsis "HDF5 library as an R package")
+    (description "This package provides C and C++ HDF5 libraries for use in R
+packages.")
+    (license license:artistic2.0)))
+
+(define-public r-beachmat
+  (package
+    (name "r-beachmat")
+    (version "1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "beachmat" version))
+       (sha256
+        (base32
+         "0b6dzja5fbx4dawb7ixj67mlhw4fy62pfp20mfp918fy96zmdwqz"))))
+    (build-system r-build-system)
+    (inputs
+     `(("hdf5" ,hdf5)))
+    (propagated-inputs
+     `(("r-delayedarray" ,r-delayedarray)
+       ("r-hdf5array" ,r-hdf5array)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rhdf5" ,r-rhdf5)
+       ("r-rhdf5lib" ,r-rhdf5lib)))
+    (home-page "https://bioconductor.org/packages/beachmat")
+    (synopsis "Compiling Bioconductor to handle each matrix type")
+    (description "This package provides a consistent C++ class interface for a
+variety of commonly used matrix types, including sparse and HDF5-backed
+matrices.")
+    (license license:gpl3)))
+
+(define-public r-singlecellexperiment
+  (package
+    (name "r-singlecellexperiment")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "SingleCellExperiment" version))
+       (sha256
+        (base32
+         "1r276i97w64a5vdlg6952gkj7bls909p42zl8fn8yz87cdwyaars"))))
+    (properties
+     `((upstream-name . "SingleCellExperiment")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (home-page "https://bioconductor.org/packages/SingleCellExperiment")
+    (synopsis "S4 classes for single cell data")
+    (description "This package defines an S4 class for storing data from
+single-cell experiments.  This includes specialized methods to store and
+retrieve spike-in information, dimensionality reduction coordinates and size
+factors for each cell, along with the usual metadata for genes and
+libraries.")
+    (license license:gpl3)))
+
+(define-public r-scater
+  (package
+    (name "r-scater")
+    (version "1.6.3")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "scater" version))
+              (sha256
+               (base32
+                "0q3s96gf8saa1dq2fvmpl0jyj7bx3wrdfck3hanb8pxkcir2p7dn"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-beachmat" ,r-beachmat)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biomart" ,r-biomart)
+       ("r-data-table" ,r-data-table)
+       ("r-dplyr" ,r-dplyr)
+       ("r-edger" ,r-edger)
+       ("r-ggbeeswarm" ,r-ggbeeswarm)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-limma" ,r-limma)
+       ("r-matrix" ,r-matrix)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-plyr" ,r-plyr)
+       ("r-rcpp" ,r-rcpp)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rhdf5" ,r-rhdf5)
+       ("r-rhdf5lib" ,r-rhdf5lib)
+       ("r-rjson" ,r-rjson)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-shiny" ,r-shiny)
+       ("r-shinydashboard" ,r-shinydashboard)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-tximport" ,r-tximport)
+       ("r-viridis" ,r-viridis)))
+    (home-page "https://github.com/davismcc/scater")
+    (synopsis "Single-cell analysis toolkit for gene expression data in R")
+    (description "This package provides a collection of tools for doing
+various analyses of single-cell RNA-seq gene expression data, with a focus on
+quality control.")
+    (license license:gpl2+)))
+
+(define-public r-scran
+  (package
+    (name "r-scran")
+    (version "1.6.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "scran" version))
+       (sha256
+        (base32
+         "0zfm5i8xrnzb3894xygqd6zkbwaa2x3z74wbxw39fcjhyhxv2hmb"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-beachmat" ,r-beachmat)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-dt" ,r-dt)
+       ("r-dynamictreecut" ,r-dynamictreecut)
+       ("r-edger" ,r-edger)
+       ("r-fnn" ,r-fnn)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-igraph" ,r-igraph)
+       ("r-limma" ,r-limma)
+       ("r-matrix" ,r-matrix)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rhdf5lib" ,r-rhdf5lib)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scater" ,r-scater)
+       ("r-shiny" ,r-shiny)
+       ("r-singlecellexperiment" ,r-singlecellexperiment)
+       ("r-statmod" ,r-statmod)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-viridis" ,r-viridis)
+       ("r-zoo" ,r-zoo)))
+    (home-page "https://bioconductor.org/packages/scran")
+    (synopsis "Methods for single-cell RNA-Seq data analysis")
+    (description "This package implements a variety of low-level analyses of
+single-cell RNA-seq data.  Methods are provided for normalization of
+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
@@ -11106,3 +11398,491 @@ for alignment.  Pseudoalignment of reads preserves the key information needed
 for quantification, and kallisto is therefore not only fast, but also as
 accurate as existing quantification tools.")
     (license license:bsd-2)))
+
+(define-public libgff
+  (package
+    (name "libgff")
+    (version "1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/Kingsford-Group/"
+                    "libgff/archive/v" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0vc4nxyhlm6g9vvmx5l4lfs5pnvixsv1hiiy4kddf2y3p6jna8ls"))))
+    (build-system cmake-build-system)
+    (arguments `(#:tests? #f))          ; no tests included
+    (home-page "https://github.com/Kingsford-Group/libgff")
+    (synopsis "Parser library for reading/writing GFF files")
+    (description "This is a simple \"libraryfication\" of the GFF/GTF parsing
+code that is used in the Cufflinks codebase.  The goal of this library is to
+provide this functionality without the necessity of drawing in a heavy-weight
+dependency like SeqAn.")
+    (license (license:x11-style "http://www.boost.org/LICENSE_1_0.txt"))))
+
+(define-public libdivsufsort
+  (package
+    (name "libdivsufsort")
+    (version "2.0.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/y-256/libdivsufsort.git")
+                    (commit version)))
+              (sha256
+               (base32
+                "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:tests? #f                      ; there are no tests
+       #:configure-flags
+       ;; Needed for rapmap and sailfish.
+       '("-DBUILD_DIVSUFSORT64=ON")))
+    (home-page "https://github.com/y-256/libdivsufsort")
+    (synopsis "Lightweight suffix-sorting library")
+    (description "libdivsufsort is a software library that implements a
+lightweight suffix array construction algorithm.  This library provides a
+simple and an efficient C API to construct a suffix array and a
+Burrows-Wheeler transformed string from a given string over a constant-size
+alphabet.  The algorithm runs in O(n log n) worst-case time using only 5n+O(1)
+bytes of memory space, where n is the length of the string.")
+    (license license:expat)))
+
+(define-public sailfish
+  (package
+    (name "sailfish")
+    (version "0.10.1")
+    (source (origin
+              (method url-fetch)
+              (uri
+               (string-append "https://github.com/kingsfordgroup/"
+                              "sailfish/archive/v" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1inn60dxiwsz8g9w7kvfhjxj4bwfb0r12dyhpzzhfbig712dkmm0"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Delete bundled headers for eigen3.
+                  (delete-file-recursively "include/eigen3/")
+                  #t))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+       (list (string-append "-DBOOST_INCLUDEDIR="
+                            (assoc-ref %build-inputs "boost")
+                            "/include/")
+             (string-append "-DBOOST_LIBRARYDIR="
+                            (assoc-ref %build-inputs "boost")
+                            "/lib/")
+             (string-append "-DBoost_LIBRARIES="
+                            "-lboost_iostreams "
+                            "-lboost_filesystem "
+                            "-lboost_system "
+                            "-lboost_thread "
+                            "-lboost_timer "
+                            "-lboost_chrono "
+                            "-lboost_program_options")
+             "-DBoost_FOUND=TRUE"
+             ;; Don't download RapMap---we already have it!
+             "-DFETCHED_RAPMAP=1")
+       ;; Tests must be run after installation and the location of the test
+       ;; data file must be overridden.  But the tests fail.  It looks like
+       ;; they are not really meant to be run.
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         ;; Boost cannot be found, even though it's right there.
+         (add-after 'unpack 'do-not-look-for-boost
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "CMakeLists.txt"
+               (("find_package\\(Boost 1\\.53\\.0") "#"))))
+         (add-after 'unpack 'do-not-assign-to-macro
+           (lambda _
+             (substitute* "include/spdlog/details/format.cc"
+               (("const unsigned CHAR_WIDTH = 1;") ""))))
+         (add-after 'unpack 'prepare-rapmap
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((src "external/install/src/rapmap/")
+                   (include "external/install/include/rapmap/")
+                   (rapmap (assoc-ref inputs "rapmap")))
+               (mkdir-p "/tmp/rapmap")
+               (system* "tar" "xf"
+                        (assoc-ref inputs "rapmap")
+                        "-C" "/tmp/rapmap"
+                        "--strip-components=1")
+               (mkdir-p src)
+               (mkdir-p include)
+               (for-each (lambda (file)
+                           (install-file file src))
+                         (find-files "/tmp/rapmap/src" "\\.(c|cpp)"))
+               (copy-recursively "/tmp/rapmap/include" include))))
+         (add-after 'unpack 'use-system-libraries
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* '("src/SailfishIndexer.cpp"
+                            "src/SailfishUtils.cpp"
+                            "src/SailfishQuantify.cpp"
+                            "src/FASTAParser.cpp"
+                            "include/PCA.hpp"
+                            "include/SailfishUtils.hpp"
+                            "include/SailfishIndex.hpp"
+                            "include/CollapsedEMOptimizer.hpp"
+                            "src/CollapsedEMOptimizer.cpp")
+               (("#include \"jellyfish/config.h\"") ""))
+             (substitute* "src/CMakeLists.txt"
+               (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..")
+                (string-append (assoc-ref inputs "jellyfish")
+                               "/include/jellyfish-" ,(package-version jellyfish)))
+               (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a")
+                (string-append (assoc-ref inputs "jellyfish")
+                               "/lib/libjellyfish-2.0.a"))
+               (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a")
+                (string-append (assoc-ref inputs "libdivsufsort")
+                               "/lib/libdivsufsort.so"))
+               (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a")
+                (string-append (assoc-ref inputs "libdivsufsort")
+                               "/lib/libdivsufsort64.so")))
+             (substitute* "CMakeLists.txt"
+               ;; Don't prefer static libs
+               (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
+               (("find_package\\(Jellyfish.*") "")
+               (("ExternalProject_Add\\(libjellyfish") "message(")
+               (("ExternalProject_Add\\(libgff") "message(")
+               (("ExternalProject_Add\\(libsparsehash") "message(")
+               (("ExternalProject_Add\\(libdivsufsort") "message("))
+
+             ;; Ensure that Eigen headers can be found
+             (setenv "CPLUS_INCLUDE_PATH"
+                     (string-append (getenv "CPLUS_INCLUDE_PATH")
+                                    ":"
+                                    (assoc-ref inputs "eigen")
+                                    "/include/eigen3")))))))
+    (inputs
+     `(("boost" ,boost)
+       ("eigen" ,eigen)
+       ("jemalloc" ,jemalloc)
+       ("jellyfish" ,jellyfish)
+       ("sparsehash" ,sparsehash)
+       ("rapmap" ,(origin
+                    (method git-fetch)
+                    (uri (git-reference
+                          (url "https://github.com/COMBINE-lab/RapMap.git")
+                          (commit (string-append "sf-v" version))))
+                    (file-name (string-append "rapmap-sf-v" version "-checkout"))
+                    (sha256
+                     (base32
+                      "1hv79l5i576ykv5a1srj2p0q36yvyl5966m0fcy2lbi169ipjakf"))
+                    (modules '((guix build utils)))
+                    ;; These files are expected to be excluded.
+                    (snippet
+                     '(begin (delete-file-recursively "include/spdlog")
+                             (for-each delete-file '("include/xxhash.h"
+                                                     "src/xxhash.c"))))))
+       ("libdivsufsort" ,libdivsufsort)
+       ("libgff" ,libgff)
+       ("tbb" ,tbb)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "http://www.cs.cmu.edu/~ckingsf/software/sailfish")
+    (synopsis "Mapping-based isoform quantification from RNA-Seq reads")
+    (description "Sailfish is a tool for genomic transcript quantification
+from RNA-seq data.  It requires a set of target transcripts (either from a
+reference or de-novo assembly) to quantify.  All you need to run sailfish is a
+fasta file containing your reference transcripts and a (set of) fasta/fastq
+file(s) containing your reads.")
+    (license license:gpl3+)))
+
+(define libstadenio-for-salmon
+  (package
+    (name "libstadenio")
+    (version "1.14.8")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/COMBINE-lab/staden-io_lib.git")
+                    (commit (string-append "v" version))))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "1x8kxxqxl892vwfbprlbyfwkkv7c34ggkc94892x9x0g37x5nbwx"))))
+    (build-system gnu-build-system)
+    (arguments '(#:parallel-tests? #f)) ; not supported
+    (inputs
+     `(("zlib" ,zlib)))
+    (native-inputs
+     `(("perl" ,perl)))                 ; for tests
+    (home-page "https://github.com/COMBINE-lab/staden-io_lib")
+    (synopsis "General purpose trace and experiment file library")
+    (description "This package provides a library of file reading and writing
+code to provide a general purpose Trace file (and Experiment File) reading
+interface.
+
+The following file formats are supported:
+
+@enumerate
+@item SCF trace files
+@item ABI trace files
+@item ALF trace files
+@item ZTR trace files
+@item SFF trace archives
+@item SRF trace archives
+@item Experiment files
+@item Plain text files
+@item SAM/BAM sequence files
+@item CRAM sequence files
+@end enumerate\n")
+    (license license:bsd-3)))
+
+(define spdlog-for-salmon
+  (package
+    (name "spdlog")
+    (version "0.14.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/COMBINE-lab/spdlog.git")
+                    (commit (string-append "v" version))))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "13730429gwlabi432ilpnja3sfvy0nn2719vnhhmii34xcdyc57q"))))
+    (build-system cmake-build-system)
+    (home-page "https://github.com/COMBINE-lab/spdlog")
+    (synopsis "Very fast C++ logging library")
+    (description "Spdlog is a very fast header-only C++ logging library with
+performance as its primary goal.")
+    (license license:expat)))
+
+;; This is a modified variant of bwa for use with Salmon. It installs a
+;; library to avoid having to build this as part of Salmon.
+(define bwa-for-salmon
+  (package (inherit bwa)
+    (name "bwa")
+    (version "0.7.12.5")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/COMBINE-lab/bwa.git")
+                    (commit (string-append "v" version))))
+              (file-name (string-append "bwa-for-salmon-" version "-checkout"))
+              (sha256
+               (base32
+                "1z2qa64y0c5hky10510x137mnzlhz6k8qf27csw4w9j6qihq95gb"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f ;no "check" target
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (lib (string-append out "/lib"))
+                    (doc (string-append out "/share/doc/bwa"))
+                    (man (string-append out "/share/man/man1"))
+                    (inc (string-append out "/include/bwa")))
+               (install-file "bwa" bin)
+               (install-file "README.md" doc)
+               (install-file "bwa.1" man)
+               (install-file "libbwa.a" lib)
+               (mkdir-p lib)
+               (mkdir-p inc)
+               (for-each (lambda (file)
+                           (install-file file inc))
+                         (find-files "." "\\.h$")))
+             #t))
+         ;; no "configure" script
+         (delete 'configure))))))
+
+(define-public salmon
+  (package
+    (name "salmon")
+    (version "0.9.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/COMBINE-lab/salmon.git")
+                    (commit (string-append "v" version))))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "1zi1ff4i7y2ykk0vdzysgwzzzv166vg2x77pj1mf4baclavxj87a"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Delete bundled headers for eigen3.
+                  (delete-file-recursively "include/eigen3/")
+                  #t))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+       (list (string-append "-DBOOST_INCLUDEDIR="
+                            (assoc-ref %build-inputs "boost")
+                            "/include/")
+             (string-append "-DBOOST_LIBRARYDIR="
+                            (assoc-ref %build-inputs "boost")
+                            "/lib/")
+             (string-append "-DBoost_LIBRARIES="
+                            "-lboost_iostreams "
+                            "-lboost_filesystem "
+                            "-lboost_system "
+                            "-lboost_thread "
+                            "-lboost_timer "
+                            "-lboost_chrono "
+                            "-lboost_program_options")
+             "-DBoost_FOUND=TRUE"
+             "-DTBB_LIBRARIES=tbb tbbmalloc"
+             ;; Don't download RapMap---we already have it!
+             "-DFETCHED_RAPMAP=1")
+       #:phases
+       (modify-phases %standard-phases
+         ;; Boost cannot be found, even though it's right there.
+         (add-after 'unpack 'do-not-look-for-boost
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "CMakeLists.txt"
+               (("find_package\\(Boost 1\\.53\\.0") "#"))))
+         (add-after 'unpack 'do-not-phone-home
+           (lambda _
+             (substitute* "src/Salmon.cpp"
+               (("getVersionMessage\\(\\)") "\"\""))))
+         (add-after 'unpack 'prepare-rapmap
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((src "external/install/src/rapmap/")
+                   (include "external/install/include/rapmap/")
+                   (rapmap (assoc-ref inputs "rapmap")))
+               (mkdir-p src)
+               (mkdir-p include)
+               (for-each (lambda (file)
+                           (install-file file src))
+                         (find-files (string-append rapmap "/src") "\\.(c|cpp)"))
+               (copy-recursively (string-append rapmap "/include") include)
+               (for-each delete-file '("external/install/include/rapmap/xxhash.h"
+                                       "external/install/include/rapmap/FastxParser.hpp"
+                                       "external/install/include/rapmap/concurrentqueue.h"
+                                       "external/install/include/rapmap/FastxParserThreadUtils.hpp"
+                                       "external/install/src/rapmap/FastxParser.cpp"
+                                       "external/install/src/rapmap/xxhash.c")))))
+         (add-after 'unpack 'use-system-libraries
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "src/CMakeLists.txt"
+               (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..")
+                (string-append (assoc-ref inputs "jellyfish")
+                               "/include/jellyfish-" ,(package-version jellyfish)))
+               (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a")
+                (string-append (assoc-ref inputs "jellyfish")
+                               "/lib/libjellyfish-2.0.a"))
+               (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a")
+                (string-append (assoc-ref inputs "libdivsufsort")
+                               "/lib/libdivsufsort.so"))
+               (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libstaden-read.a")
+                (string-append (assoc-ref inputs "libstadenio-for-salmon")
+                               "/lib/libstaden-read.a"))
+               (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libbwa.a")
+                (string-append (assoc-ref inputs "bwa") "/lib/libbwa.a"))
+               (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a")
+                (string-append (assoc-ref inputs "libdivsufsort")
+                               "/lib/libdivsufsort64.so")))
+             (substitute* "CMakeLists.txt"
+               ;; Don't prefer static libs
+               (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
+               (("set\\(TBB_LIBRARIES") "message(")
+               (("find_package\\(Jellyfish.*") "")
+               (("ExternalProject_Add\\(libcereal") "message(")
+               (("ExternalProject_Add\\(libbwa") "message(")
+               (("ExternalProject_Add\\(libjellyfish") "message(")
+               (("ExternalProject_Add\\(libgff") "message(")
+               (("ExternalProject_Add\\(libtbb") "message(")
+               (("ExternalProject_Add\\(libspdlog") "message(")
+               (("ExternalProject_Add\\(libdivsufsort") "message(")
+               (("ExternalProject_Add\\(libstadenio") "message(")
+               (("ExternalProject_Add_Step\\(") "message("))
+
+             ;; Ensure that all headers can be found
+             (setenv "CPLUS_INCLUDE_PATH"
+                     (string-append (getenv "CPLUS_INCLUDE_PATH")
+                                    ":"
+                                    (assoc-ref inputs "bwa")
+                                    "/include/bwa"
+                                    ":"
+                                    (assoc-ref inputs "eigen")
+                                    "/include/eigen3"))
+             (setenv "CPATH"
+                     (string-append (assoc-ref inputs "bwa")
+                                    "/include/bwa"
+                                    ":"
+                                    (assoc-ref inputs "eigen")
+                                    "/include/eigen3"))
+             #t))
+         ;; CMAKE_INSTALL_PREFIX does not exist when the tests are
+         ;; run.  It only exists after the install phase.
+         (add-after 'unpack 'fix-tests
+           (lambda _
+             (substitute* "src/CMakeLists.txt"
+               (("DTOPLEVEL_DIR=\\$\\{CMAKE_INSTALL_PREFIX")
+                "DTOPLEVEL_DIR=${GAT_SOURCE_DIR"))
+             #t)))))
+    (inputs
+     `(("boost" ,boost)
+       ("bwa" ,bwa-for-salmon)
+       ("bzip2" ,bzip2)
+       ("cereal" ,cereal)
+       ("eigen" ,eigen)
+       ("rapmap" ,(origin
+                    (method git-fetch)
+                    (uri (git-reference
+                          (url "https://github.com/COMBINE-lab/RapMap.git")
+                          (commit (string-append "salmon-v" version))))
+                    (file-name (string-append "rapmap-salmon-v" version "-checkout"))
+                    (sha256
+                     (base32
+                      "1yc12yqsz6f0r8sg1qnk57xg34aqwc9jbqq6gd5ys28xw3plj98p"))))
+       ("jemalloc" ,jemalloc)
+       ("jellyfish" ,jellyfish)
+       ("libgff" ,libgff)
+       ("tbb" ,tbb)
+       ("libdivsufsort" ,libdivsufsort)
+       ("libstadenio-for-salmon" ,libstadenio-for-salmon)
+       ("spdlog-for-salmon" ,spdlog-for-salmon)
+       ("xz" ,xz)
+       ("zlib" ,zlib)))
+    (home-page "https://github.com/COMBINE-lab/salmon")
+    (synopsis "Quantification from RNA-seq reads using lightweight alignments")
+    (description "Salmon is a program to produce highly-accurate,
+transcript-level quantification estimates from RNA-seq data.  Salmon achieves
+its accuracy and speed via a number of different innovations, including the
+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)))