gnu: r-genefilter: Update to 1.62.0.

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9239f08..2df630d 100644 (file)
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -252,7 +252,7 @@ instance, it implements several methods to assess contig-wise read coverage.")
 (define-public bamtools
   (package
     (name "bamtools")
-    (version "2.4.1")
+    (version "2.5.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -261,7 +261,7 @@ instance, it implements several methods to assess contig-wise read coverage.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0jr024kcrhjb82cm69i7p5fcg5375zlc1h3qh2n1v368hcd0qflk"))))
+                "1z3kg24qrwq13a88n9d86izngrar4fll7gr6phddb2faw75pdgaa"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ;no "check" target
@@ -2079,7 +2079,7 @@ accurately delineate genomic rearrangements throughout the genome.")
 (define-public diamond
   (package
     (name "diamond")
-    (version "0.9.21")
+    (version "0.9.22")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2088,7 +2088,7 @@ accurately delineate genomic rearrangements throughout the genome.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1cf98vcsiwcv3c4apg50w1240v1mpw0zln1sdw3g692dqa4y041z"))))
+                "0adp87r9ak63frdrdmrdfhsn6g0jnnyq1lr2wibvqbxcl37iir9m"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; no "check" target
@@ -2339,7 +2339,8 @@ dynamic programming or a variety of heuristics.")
                 (string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
              (substitute* "src/CMakeLists.txt"
                (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
-                (string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
+                (string-append (assoc-ref inputs "bamtools") "/lib"))
+               (("libprotobuf.a") "libprotobuf.so"))
              #t)))))
     (inputs
      `(("boost" ,boost)
@@ -3449,6 +3450,42 @@ The main functions of FastQC are:
 @end itemize\n")
     (license license:gpl3+)))
 
+(define-public fastp
+  (package
+    (name "fastp")
+    (version "0.14.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/OpenGene/fastp.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1r6ms5zbf5rps4rgp4z73nczadl00b5rqylw8f684isfz27dp0xh"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; there are none
+       #:make-flags
+       (list (string-append "BINDIR=" (assoc-ref %outputs "out") "/bin"))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-before 'install 'create-target-dir
+           (lambda* (#:key outputs #:allow-other-keys)
+             (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
+             #t)))))
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://github.com/OpenGene/fastp/")
+    (synopsis "All-in-one FastQ preprocessor")
+    (description
+     "Fastp is a tool designed to provide fast all-in-one preprocessing for
+FastQ files.  This tool has multi-threading support to afford high
+performance.")
+    (license license:expat)))
+
 (define-public htslib
   (package
     (name "htslib")
@@ -4574,7 +4611,7 @@ partial genes, and identifies translation initiation sites.")
 (define-public roary
   (package
     (name "roary")
-    (version "3.11.0")
+    (version "3.12.0")
     (source
      (origin
        (method url-fetch)
@@ -4583,7 +4620,7 @@ partial genes, and identifies translation initiation sites.")
              version ".tar.gz"))
        (sha256
         (base32
-         "10lw78x1xzvn7xzvnmh4bm3cak3ah5cssapl0yidvhaj1f44h29i"))))
+         "0qxrds9wx7cfhlkihrp6697kx0flhhxymap9fwan0b3rbdhcnmff"))))
     (build-system perl-build-system)
     (arguments
      `(#:phases
@@ -5768,7 +5805,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
 (define-public star
   (package
     (name "star")
-    (version "2.5.3a")
+    (version "2.6.0a")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/alexdobin/STAR/archive/"
@@ -5776,7 +5813,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "013wirlz8lllgjyagl48l75n1isxyabqb3sj7qlsl0x1rmvqw99a"))
+                "0yci4ymy4407kjh0lqp021nzccp6r31wgrkixkmix5p130cxvc56"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -6082,20 +6119,20 @@ information as possible.")
 (define-public r-vegan
   (package
     (name "r-vegan")
-    (version "2.5-1")
+    (version "2.5-2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vegan" version))
        (sha256
         (base32
-         "0pynr02d1xngda6c3va8fc4nxpgfkawhzcnz1ws4dnarp9b1w90r"))))
+         "13pyqvlpz64qibi8k5d109v7q09j06mbv6ndix3n4cn21mjx391c"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
     (propagated-inputs
      `(("r-cluster" ,r-cluster)
-       ("r-knitr" ,r-knitr)
+       ("r-knitr" ,r-knitr) ; needed for vignettes
        ("r-lattice" ,r-lattice)
        ("r-mass" ,r-mass)
        ("r-mgcv" ,r-mgcv)
@@ -6112,14 +6149,14 @@ data types as well.")
 (define-public r-annotate
   (package
     (name "r-annotate")
-    (version "1.56.2")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "annotate" version))
        (sha256
         (base32
-         "0ybg9k1s289h15nj1kp9821i1rsk1gkn8i8blplmk7gsgpbw1f42"))))
+         "1qmncyvy147a1ll3iri45p822kcs3s7583jfnq9jf6sz9ilk8cjf"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotationdbi" ,r-annotationdbi)
@@ -6139,13 +6176,13 @@ microarrays.")
 (define-public r-copynumber
   (package
     (name "r-copynumber")
-    (version "1.18.0")
+    (version "1.20.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "copynumber" version))
               (sha256
                (base32
-                "01kcwzl485yjrkgyg8117b1il957ss0v6rq4bbxf4ksd5fzcjmyx"))))
+                "0y9nnwb0psphp3ix88wj2f8z5gr45r5znf55w892ysm27isdpmms"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-s4vectors" ,r-s4vectors)
@@ -6162,14 +6199,14 @@ penalized least squares regression method.")
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
-    (version "1.56.0")
+    (version "1.58.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "geneplotter" version))
        (sha256
         (base32
-         "1z3g7frc1iviwrsv2dlm4nqvkc0685h4va0388yfxn102ln8wwma"))))
+         "055g28xgiazl4l0gkg8xiamks64f5yckjjyvw1abd6d6qjavwx0g"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-annotate" ,r-annotate)
@@ -6187,14 +6224,14 @@ penalized least squares regression method.")
 (define-public r-genefilter
   (package
     (name "r-genefilter")
-    (version "1.60.0")
+    (version "1.62.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "genefilter" version))
        (sha256
         (base32
-         "173swlg6gj4kdllbqvyiw5dggbcxiwlwpqmllsv4dxzn7h25i3g7"))))
+         "14l0ff02spmjwxj0m1czhg5vlkgwcfi73cym8m2n9vn6i7bjdaqi"))))
     (build-system r-build-system)
     (native-inputs
      `(("gfortran" ,gfortran)))
@@ -9062,14 +9099,14 @@ replacement for strverscmp.")
 (define-public multiqc
   (package
     (name "multiqc")
-    (version "1.4")
+    (version "1.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "multiqc" version))
        (sha256
         (base32
-         "0ihx4rzmsfphv4byn05qv6f1y95g2dxs6viwziipl4wjk96acgm8"))))
+         "02iihfl0w0hpnr4pa0sbd1y9qxrg3ycyhjp5lidkcrqh1lmzs3zy"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-jinja2" ,python-jinja2)
@@ -9084,6 +9121,19 @@ replacement for strverscmp.")
        ("python-numpy" ,python-numpy)
        ;; MultQC checks for the presence of nose at runtime.
        ("python-nose" ,python-nose)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'relax-requirements
+           (lambda _
+             (substitute* "setup.py"
+               ;; MultiQC 1.5 ‘requires’ a version of python-matplotlib older
+               ;; than the one in Guix, but should work fine with 2.2.2.
+               ;; See <https://github.com/ewels/MultiQC/issues/725> and
+               ;; <https://github.com/ewels/MultiQC/issues/732> for details.
+               (("['\"]matplotlib.*?['\"]")
+                "'matplotlib'"))
+             #t)))))
     (home-page "http://multiqc.info")
     (synopsis "Aggregate bioinformatics analysis reports")
     (description
@@ -9637,13 +9687,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
 (define-public r-seurat
   (package
     (name "r-seurat")
-    (version "2.3.0")
+    (version "2.3.1")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "Seurat" version))
               (sha256
                (base32
-                "0kp3lw1s896zkjd6x2wp8qcg7wnm5b40g8vihps13f1m7j4nx7r0"))
+                "0hi59rgdrr2iqfvx5bq7yq02hbjxkjl1fzidqj14z0ypq0nzbjys"))
               ;; Delete pre-built jar.
               (snippet
                '(begin (delete-file "inst/java/ModularityOptimizer.jar")
@@ -9687,7 +9737,6 @@ Main-Class: ModularityOptimizer\n")))
        ("r-ggplot2" ,r-ggplot2)
        ("r-ggridges" ,r-ggridges)
        ("r-gplots" ,r-gplots)
-       ("r-gridextra" ,r-gridextra)
        ("r-hmisc" ,r-hmisc)
        ("r-ica" ,r-ica)
        ("r-igraph" ,r-igraph)
@@ -9708,6 +9757,7 @@ Main-Class: ModularityOptimizer\n")))
        ("r-rcppeigen" ,r-rcppeigen)
        ("r-rcppprogress" ,r-rcppprogress)
        ("r-reshape2" ,r-reshape2)
+       ("r-reticulate" ,r-reticulate)
        ("r-rocr" ,r-rocr)
        ("r-rtsne" ,r-rtsne)
        ("r-sdmtools" ,r-sdmtools)
@@ -11140,25 +11190,22 @@ with narrow binding events such as transcription factor ChIP-seq.")
 (define-public trim-galore
   (package
     (name "trim-galore")
-    (version "0.4.2")
+    (version "0.4.5")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "http://www.bioinformatics.babraham.ac.uk/"
-                           "projects/trim_galore/trim_galore_v"
-                           version ".zip"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/FelixKrueger/TrimGalore.git")
+             (commit version)))
+       (file-name (string-append name "-" version "-checkout"))
        (sha256
         (base32
-         "0b9qdxi4521gsrjvbhgky8g7kry9b5nx3byzaxkgxz7p4k8bn1mn"))))
+         "0x5892l48c816pf00wmnz5vq0zq6170d3xc8zrxncd4jcz7h1p71"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f                      ; no tests
        #:phases
        (modify-phases %standard-phases
-         ;; The archive contains plain files.
-         (replace 'unpack
-           (lambda* (#:key source #:allow-other-keys)
-             (zero? (system* "unzip" source))))
          (delete 'configure)
          (delete 'build)
          (add-after 'unpack 'hardcode-tool-references
@@ -11539,7 +11586,9 @@ browser.")
            (replace 'install
              (lambda* (#:key inputs outputs #:allow-other-keys)
                (let* ((target (assoc-ref outputs "out"))
-                      (doc (string-append target "/share/doc/f-seq/")))
+                      (bin (string-append target "/bin"))
+                      (doc (string-append target "/share/doc/f-seq"))
+                      (lib (string-append target "/lib")))
                  (mkdir-p target)
                  (mkdir-p doc)
                  (substitute* "bin/linux/fseq"
@@ -11548,11 +11597,11 @@ browser.")
                     (string-append (assoc-ref inputs "java-commons-cli")
                                    "/share/java/commons-cli.jar"))
                    (("REALDIR=.*")
-                    (string-append "REALDIR=" target "/bin\n")))
+                    (string-append "REALDIR=" bin "\n")))
                  (install-file "README.txt" doc)
-                 (install-file "bin/linux/fseq" (string-append target "/bin"))
-                 (install-file "build~/fseq.jar" (string-append target "/lib"))
-                 (copy-recursively "lib" (string-append target "/lib"))
+                 (install-file "bin/linux/fseq" bin)
+                 (install-file "build~/fseq.jar" lib)
+                 (copy-recursively "lib" lib)
                  #t))))))
       (inputs
        `(("perl" ,perl)
@@ -11570,47 +11619,61 @@ Browser.")
 (define-public bismark
   (package
     (name "bismark")
-    (version "0.16.3")
+    (version "0.19.1")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/FelixKrueger/Bismark/"
-                           "archive/" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/FelixKrueger/Bismark.git")
+             (commit version)))
+       (file-name (string-append name "-" version "-checkout"))
        (sha256
         (base32
-         "1204i0pa02ll2jn5pnxypkclnskvv7a2nwh5nxhagmhxk9wfv9sq"))))
+         "0yb5l36slwg02fp4b1jdlplgljcsxgqfzvzihzdnphd87dghcc84"))
+       (snippet
+        '(begin
+           ;; highcharts.js is non-free software.  The code is available under
+           ;; CC-BY-NC or proprietary licenses only.
+           (delete-file "bismark_sitrep/highcharts.js")
+           #t))))
     (build-system perl-build-system)
     (arguments
-     `(#:tests? #f ; there are no tests
+     `(#:tests? #f                      ; there are no tests
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
          (delete 'build)
          (replace 'install
            (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let ((bin (string-append (assoc-ref outputs "out")
-                                       "/bin"))
-                   (docdir  (string-append (assoc-ref outputs "out")
-                                           "/share/doc/bismark"))
-                   (docs    '("Bismark_User_Guide.pdf"
-                              "RELEASE_NOTES.txt"))
-                   (scripts '("bismark"
-                              "bismark_genome_preparation"
-                              "bismark_methylation_extractor"
-                              "bismark2bedGraph"
-                              "bismark2report"
-                              "coverage2cytosine"
-                              "deduplicate_bismark"
-                              "bismark_sitrep.tpl"
-                              "bam2nuc"
-                              "bismark2summary")))
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (share   (string-append out "/share/bismark"))
+                    (docdir  (string-append out "/share/doc/bismark"))
+                    (docs    '("Docs/Bismark_User_Guide.html"))
+                    (scripts '("bismark"
+                               "bismark_genome_preparation"
+                               "bismark_methylation_extractor"
+                               "bismark2bedGraph"
+                               "bismark2report"
+                               "coverage2cytosine"
+                               "deduplicate_bismark"
+                               "filter_non_conversion"
+                               "bam2nuc"
+                               "bismark2summary")))
+               (substitute* "bismark2report"
+                 (("\\$RealBin/bismark_sitrep")
+                  (string-append share "/bismark_sitrep")))
+               (mkdir-p share)
                (mkdir-p docdir)
                (mkdir-p bin)
                (for-each (lambda (file) (install-file file bin))
                          scripts)
                (for-each (lambda (file) (install-file file docdir))
                          docs)
+               (copy-recursively "Docs/Images" (string-append docdir "/Images"))
+               (copy-recursively "bismark_sitrep"
+                                 (string-append share "/bismark_sitrep"))
+
                ;; Fix references to gunzip
                (substitute* (map (lambda (file)
                                    (string-append bin "/" file))
@@ -11737,7 +11800,7 @@ accurate as existing quantification tools.")
 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"))))
+    (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt"))))
 
 (define-public libdivsufsort
   (package
@@ -12968,7 +13031,7 @@ methylation and segmentation.")
 (define-public pigx-scrnaseq
   (package
     (name "pigx-scrnaseq")
-    (version "0.0.3")
+    (version "0.0.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
@@ -12976,7 +13039,7 @@ methylation and segmentation.")
                                   "/pigx_scrnaseq-" version ".tar.gz"))
               (sha256
                (base32
-                "12qdq0nj1wdkyighdxj6924bmbpd1a0b3gam6w64l4hiqrv5sijz"))))
+                "1pvjm6f3mascprs65vflggwwg5v925knvgal7k7a6nnlmw5qndrf"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags