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

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Mathieu Othacehe 2021-10-12 16:50:47 +00:00
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@ -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