Merge remote-tracking branch 'origin/master' into core-updates-frozen.

1 files changed, 139 insertions, 24 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d91ff13b46..7b41c06bf6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -21,6 +21,7 @@
 ;;; Copyright © 2020 Bonface Munyoki Kilyungi <bonfacemunyoki@gmail.com>
 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
+;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -106,7 +107,6 @@
   #:use-module (gnu packages jemalloc)
   #:use-module (gnu packages jupyter)
   #:use-module (gnu packages linux)
-  #:use-module (gnu packages lisp-xyz)
   #:use-module (gnu packages logging)
   #:use-module (gnu packages lsof)
   #:use-module (gnu packages machine-learning)
@@ -148,6 +148,7 @@
   #:use-module (gnu packages textutils)
   #:use-module (gnu packages time)
   #:use-module (gnu packages tls)
+  #:use-module (gnu packages uglifyjs)
   #:use-module (gnu packages vim)
   #:use-module (gnu packages web)
   #:use-module (gnu packages wget)
@@ -2323,7 +2324,13 @@ databases.")
              (let ((out (assoc-ref outputs "out")))
                (for-each make-file-writable
                          (find-files out "\\.gz$"))
-               #t))))))
+               #t)))
+         (add-after 'unpack 'disable-nondeterministic-test
+           (lambda _
+             ;; This test fails/succeeds non-deterministically.
+             (substitute* "clipper/test/test_call_peak.py"
+               (("test_get_FDR_cutoff_mean") "_test_get_FDR_cutoff_mean"))
+             #t)))))
     (inputs
      `(("htseq" ,htseq)
        ("python-pybedtools" ,python-pybedtools)
@@ -7351,6 +7358,39 @@ sequence.")
     (supported-systems '("i686-linux" "x86_64-linux"))
     (license license:bsd-3)))
 
+(define-public r-presto
+  (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad")
+        (revision "0"))
+    (package
+      (name "r-presto")
+      (version (git-version "1.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/immunogenomics/presto")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1c3fmag4r4p2lvbvxlxyck9dvfw1prbwcl9665mmlx4a35750hk8"))))
+      (properties `((upstream . "presto")))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-data-table" ,r-data-table)
+         ("r-deseq2" ,r-deseq2)
+         ("r-dplyr" ,r-dplyr)
+         ("r-matrix" ,r-matrix)
+         ("r-rcpp" ,r-rcpp)
+         ("r-rcpparmadillo" ,r-rcpparmadillo)
+         ("r-reshape2" ,r-reshape2)
+         ("r-rlang" ,r-rlang)
+         ("r-tidyr" ,r-tidyr)))
+      (home-page "https://github.com/immunogenomics/presto")
+      (synopsis "Fast Functions for Differential Expression using Wilcox and AUC")
+      (description "This package performs a fast Wilcoxon rank sum test and
+auROC analysis.")
+      (license license:gpl3))))
+
 (define-public r-snapatac
   (package
     (name "r-snapatac")
@@ -9221,7 +9261,7 @@ Browser.")
            (lambda* (#:key inputs #:allow-other-keys)
              (let* ((file (assoc-ref inputs "plotly.js"))
                     (installed "plotly/plotly.js"))
-               (let ((minified (open-pipe* OPEN_READ "uglify-js" file)))
+               (let ((minified (open-pipe* OPEN_READ "uglifyjs" file)))
                  (call-with-output-file installed
                    (cut dump-port minified <>))))
              #t))
@@ -9279,7 +9319,7 @@ Browser.")
                                "v1.39.4/dist/plotly.js"))
            (sha256
             (base32 "138mwsr4nf5qif4mrxx286mpnagxd1xwl6k8aidrjgknaqg88zyr"))))
-       ("uglify-js" ,uglify-js)))
+       ("uglifyjs" ,node-uglify-js)))
     (home-page "https://www.bioinformatics.babraham.ac.uk/projects/bismark/")
     (synopsis "Map bisulfite treated sequence reads and analyze methylation")
     (description "Bismark is a program to map bisulfite treated sequencing
@@ -10389,7 +10429,8 @@ once.  This package provides tools to perform Drop-seq analyses.")
                                   "/pigx_rnaseq-" version ".tar.gz"))
               (sha256
                (base32
-                "1ja3bda1appxrzbfy7wp7khy30mm7lic8xbq3gkbpc5bld3as9cm"))))
+                "1ja3bda1appxrzbfy7wp7khy30mm7lic8xbq3gkbpc5bld3as9cm"))
+              (patches (search-patches "pigx-rnaseq-no-citeproc.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-tests? #f             ; not supported
@@ -10402,6 +10443,9 @@ once.  This package provides tools to perform Drop-seq analyses.")
              (substitute* "Makefile.in"
                (("^  tests/test_multiqc/test.sh") "")
                (("^  test.sh") ""))))
+         (add-before 'bootstrap 'autoreconf
+           (lambda _
+             (invoke "autoreconf" "-vif")))
          (add-before 'check 'set-timezone
            ;; The readr package is picky about timezones.
            (lambda* (#:key inputs #:allow-other-keys)
@@ -10441,12 +10485,13 @@ once.  This package provides tools to perform Drop-seq analyses.")
        ("r-rjson" ,r-rjson)
        ("salmon" ,salmon)
        ("pandoc" ,pandoc)
-       ("pandoc-citeproc" ,pandoc-citeproc)
        ("python-wrapper" ,python-wrapper)
        ("python-deeptools" ,python-deeptools)
        ("python-pyyaml" ,python-pyyaml)))
     (native-inputs
-     `(("tzdata" ,tzdata)))
+     `(("tzdata" ,tzdata)
+       ("automake" ,automake)
+       ("autoconf" ,autoconf)))
     (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
     (synopsis "Analysis pipeline for RNA sequencing experiments")
     (description "PiGX RNAseq is an analysis pipeline for preprocessing and
@@ -10460,7 +10505,7 @@ expression report comparing samples in an easily configurable manner.")
 (define-public pigx-chipseq
   (package
     (name "pigx-chipseq")
-    (version "0.0.52")
+    (version "0.0.53")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
@@ -10468,10 +10513,16 @@ expression report comparing samples in an easily configurable manner.")
                                   "/pigx_chipseq-" version ".tar.gz"))
               (sha256
                (base32
-                "097cvc8kr3r1nq0sgjpirzmixwjl074qp4qq3sx4ngfqi06af6r9"))))
+                "0c6npx35sszycf059w1x1k4k9hq1qqxny0i4p57q1188czr4561h"))
+              (patches (search-patches "pigx-chipseq-no-citeproc.patch"))))
     (build-system gnu-build-system)
-    ;; parts of the tests rely on access to the network
-    (arguments '(#:tests? #f))
+    (arguments
+     `(#:tests? #f ; parts of the tests rely on access to the network
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'bootstrap 'autoreconf
+           (lambda _
+             (invoke "autoreconf" "-vif"))))))
     (inputs
      `(("grep" ,grep)
        ("coreutils" ,coreutils)
@@ -10492,6 +10543,7 @@ expression report comparing samples in an easily configurable manner.")
        ("r-ggrepel" ,r-ggrepel)
        ("r-gprofiler2" ,r-gprofiler2)
        ("r-heatmaply" ,r-heatmaply)
+       ("r-hexbin" ,r-hexbin)
        ("r-htmlwidgets" ,r-htmlwidgets)
        ("r-jsonlite" ,r-jsonlite)
        ("r-pheatmap" ,r-pheatmap)
@@ -10513,7 +10565,6 @@ expression report comparing samples in an easily configurable manner.")
        ("multiqc" ,multiqc)
        ("perl" ,perl)
        ("pandoc" ,pandoc)
-       ("pandoc-citeproc" ,pandoc-citeproc)
        ("fastqc" ,fastqc)
        ("bowtie" ,bowtie)
        ("idr" ,idr)
@@ -10522,7 +10573,9 @@ expression report comparing samples in an easily configurable manner.")
        ("bedtools" ,bedtools)
        ("kentutils" ,kentutils)))
     (native-inputs
-     `(("python-pytest" ,python-pytest)))
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("python-pytest" ,python-pytest)))
     (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
     (synopsis "Analysis pipeline for ChIP sequencing experiments")
     (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak
@@ -10545,7 +10598,8 @@ in an easily configurable manner.")
                                   "/pigx_bsseq-" version ".tar.gz"))
               (sha256
                (base32
-                "05al5dacfp1vf1x3cq20jhd6w4xj5vaxslzaka6yrpg0av8sh3k3"))))
+                "05al5dacfp1vf1x3cq20jhd6w4xj5vaxslzaka6yrpg0av8sh3k3"))
+              (patches (search-patches "pigx-bsseq-no-citeproc.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(;; TODO: tests currently require 12+GB of RAM.  See
@@ -10553,6 +10607,9 @@ in an easily configurable manner.")
        #:tests? #f
        #:phases
        (modify-phases %standard-phases
+         (add-before 'bootstrap 'autoreconf
+           (lambda _
+             (invoke "autoreconf" "-vif")))
          (add-before 'check 'set-timezone
            ;; The readr package is picky about timezones.
            (lambda* (#:key inputs #:allow-other-keys)
@@ -10561,7 +10618,9 @@ in an easily configurable manner.")
                      (search-input-directory inputs
                                              "share/zoneinfo")))))))
     (native-inputs
-     `(("tzdata" ,tzdata)))
+     `(("tzdata" ,tzdata)
+       ("automake" ,automake)
+       ("autoconf" ,autoconf)))
     (inputs
      `(("coreutils" ,coreutils)
        ("sed" ,sed)
@@ -10581,7 +10640,6 @@ in an easily configurable manner.")
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggbio" ,r-ggbio)
        ("pandoc" ,pandoc)
-       ("pandoc-citeproc" ,pandoc-citeproc)
        ("python-wrapper" ,python-wrapper)
        ("python-pyyaml" ,python-pyyaml)
        ("snakemake" ,snakemake)
@@ -10614,8 +10672,18 @@ methylation and segmentation.")
                                   "/pigx_scrnaseq-" version ".tar.gz"))
               (sha256
                (base32
-                "1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx"))))
+                "1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx"))
+              (patches (search-patches "pigx-scrnaseq-no-citeproc.patch"))))
     (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'bootstrap 'autoreconf
+           (lambda _
+             (invoke "autoreconf" "-vif"))))))
+    (native-inputs
+     `(("automake" ,automake)
+       ("autoconf" ,autoconf)))
     (inputs
      `(("coreutils" ,coreutils)
        ("perl" ,perl)
@@ -10630,7 +10698,6 @@ methylation and segmentation.")
        ("python-numpy" ,python-numpy)
        ("python-loompy" ,python-loompy)
        ("pandoc" ,pandoc)
-       ("pandoc-citeproc" ,pandoc-citeproc)
        ("samtools" ,samtools)
        ("snakemake" ,snakemake)
        ("star" ,star-for-pigx)
@@ -10680,8 +10747,18 @@ based methods.")
                                   "/pigx_sars-cov2-ww-" version ".tar.gz"))
               (sha256
                (base32
-                "1hhdbwsnl0d37lrmisw5hr630xr8s41qvxflm05anh11rj8n22yw"))))
+                "1hhdbwsnl0d37lrmisw5hr630xr8s41qvxflm05anh11rj8n22yw"))
+              (patches (search-patches "pigx-sars-cov2-ww-no-citeproc.patch"))))
     (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'bootstrap 'autoreconf
+           (lambda _
+             (invoke "autoreconf" "-vif"))))))
+    (native-inputs
+     `(("automake" ,automake)
+       ("autoconf" ,autoconf)))
     (inputs
      `(("bash-minimal" ,bash-minimal)
        ("bwa" ,bwa)
@@ -12360,17 +12437,18 @@ datasets.")
 (define-public ngless
   (package
     (name "ngless")
-    (version "1.1.0")
+    (version "1.3.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
-             (url "https://gitlab.com/ngless/ngless.git")
+             (url "https://github.com/ngless-toolkit/ngless.git")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1wim8wpqyff080dfcazynrmjwqas38m24m0v350w245mmhrapdma"))))
+         "0pb9f6b0yk9p4cdwiym8r190q1bcdiwvc7i2s6rw54qgi8r3g6pj"))
+       (patches (search-patches "ngless-unliftio.patch"))))
     (build-system haskell-build-system)
     (arguments
      `(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1:
@@ -12441,7 +12519,7 @@ datasets.")
        ("ghc-http-conduit" ,ghc-http-conduit)
        ("ghc-inline-c" ,ghc-inline-c)
        ("ghc-inline-c-cpp" ,ghc-inline-c-cpp)
-       ("ghc-intervalmap" ,ghc-intervalmap)
+       ("ghc-int-interval-map" ,ghc-int-interval-map)
        ("ghc-missingh" ,ghc-missingh)
        ("ghc-optparse-applicative" ,ghc-optparse-applicative)
        ("ghc-regex" ,ghc-regex)
@@ -12468,12 +12546,49 @@ datasets.")
        ("ghc-test-framework-hunit",ghc-test-framework-hunit)
        ("ghc-test-framework-quickcheck2" ,ghc-test-framework-quickcheck2)
        ("ghc-test-framework-th" ,ghc-test-framework-th)))
-    (home-page "https://gitlab.com/ngless/ngless")
+    (home-page "https://ngless.embl.de/")
     (synopsis "DSL for processing next-generation sequencing data")
     (description "Ngless is a domain-specific language for
 @dfn{next-generation sequencing} (NGS) data processing.")
     (license license:expat)))
 
+(define-public ghc-int-interval-map
+  (let ((commit "678763de7fe6d7fa3f1c44b32d18ce58670270f4")
+        (revision "1"))
+    (package
+      (name "ghc-int-interval-map")
+      (version "0.0.0.0")
+      (source
+        (origin
+           (method git-fetch)
+           (uri (git-reference
+                 (url "https://github.com/ngless-toolkit/interval-to-int.git")
+                 (commit commit)))
+           (file-name (git-file-name name version))
+          (sha256 (base32 "0fd728b5if89vj5j4f9y7k0b2xv2ycz5a21iy15wbdcf5bhim7i8"))))
+      (build-system haskell-build-system)
+      (inputs
+        `(("ghc-either" ,ghc-either)
+          ("ghc-primitive" ,ghc-primitive)
+          ("ghc-vector" ,ghc-vector)
+          ("ghc-vector-algorithms" ,ghc-vector-algorithms)))
+      (native-inputs
+        `(("ghc-hedgehog" ,ghc-hedgehog)
+          ("ghc-tasty" ,ghc-tasty)
+          ("ghc-tasty-hedgehog" ,ghc-tasty-hedgehog)
+          ("ghc-tasty-hunit" ,ghc-tasty-hunit)
+          ("ghc-tasty-quickcheck" ,ghc-tasty-quickcheck)
+          ("ghc-tasty-th" ,ghc-tasty-th)))
+      (home-page "https://github.com/luispedro/interval-to-int#readme")
+      (synopsis "Interval map structure in Haskell")
+      (description "An interval map structure that is optimized for low
+memory (each interval is represented by about 3 words + whatever the
+cargo is) and has semantics that are appropriate for genomic intervals
+(namely, intervals can overlap and queries will return all matches
+together). It also designed to be used in two phases: a construction
+phase + query phase).")
+      (license license:expat))))
+
 (define-public filtlong
   ;; The recommended way to install is to clone the git repository
   ;; https://github.com/rrwick/Filtlong#installation