diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 163 |
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 |