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-rw-r--r--gnu/packages/bioinformatics.scm1134
1 files changed, 932 insertions, 202 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 055c8ca47b..fda01e00ca 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4,7 +4,7 @@
;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016, 2020, 2021 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016-2023 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2020, 2022 Marius Bakke <marius@gnu.org>
;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -56,7 +56,6 @@
#:use-module (guix build-system go)
#:use-module (guix build-system haskell)
#:use-module (guix build-system meson)
- #:use-module (guix build-system ocaml)
#:use-module (guix build-system perl)
#:use-module (guix build-system pyproject)
#:use-module (guix build-system python)
@@ -720,6 +719,128 @@ suite native in R.")
for all types of microbial diversity analyses.")
(license license:expat))))
+(define-public r-codeandroll2
+ (let ((commit "d58e258851a5c0b430e8620d34dbeefb597c548f")
+ (revision "1"))
+ (package
+ (name "r-codeandroll2")
+ (version (git-version "2.3.6" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vertesy/CodeAndRoll2")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0sy88mfgw6qqhpnlc5020qzr1jllkcrxfhl2lw42bkl5nb56is71"))))
+ (properties `((upstream-name . "CodeAndRoll2")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-colorramps
+ r-dplyr
+ r-gplots
+ r-gtools
+ r-plyr
+ r-rcolorbrewer
+ r-sessioninfo
+ r-sm
+ r-stringendo
+ r-stringr))
+ (home-page "https://github.com/vertesy/CodeAndRoll2")
+ (synopsis "CodeAndRoll2 for vector, matrix and list manipulations")
+ (description
+ "CodeAndRoll2 is a set of more than 130 productivity functions.
+These functions are used by MarkdownReports, ggExpress, and SeuratUtils.")
+ (license license:gpl3))))
+
+(define-public r-conospanel
+ (let ((commit "39e76b201a783b4e92fd615010a735a61746fbb9")
+ (revision "1"))
+ (package
+ (name "r-conospanel")
+ (version (git-version "1.0.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/kharchenkolab/conosPanel")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1zf0aj5d4iaxc3ghvjnaja5qby1avlmljzh94bpyvxbd359z9snn"))))
+ (properties `((upstream-name . "conosPanel")))
+ (build-system r-build-system)
+ (home-page "https://github.com/kharchenkolab/conosPanel")
+ (synopsis "Data for the conos package")
+ (description "The data within this package is a panel of four samples,
+each with 3000 cells. There are two samples which are bone marrow (BM), and
+two samples which are cord blood (CB).")
+ (license license:gpl3))))
+
+(define-public r-conqur
+ (let ((commit "c7a88794efd4ecfe4d96988dceeec3b410222e48")
+ (revision "1"))
+ (package
+ (name "r-conqur")
+ (version (git-version "2.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/wdl2459/ConQuR")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "19a7p2l67mgjy99i5ksjxlhzaqmrnyi1vzvwnhgnx2jrr6crj7rq"))))
+ (properties `((upstream-name . "ConQuR")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-ade4
+ r-ape
+ r-compositions
+ r-cqrreg
+ r-doparallel
+ r-dplyr
+ r-fastdummies
+ r-glmnet
+ r-gplots
+ r-gunifrac
+ r-quantreg
+ r-randomforest
+ r-rocr
+ r-vegan))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/wdl2459/ConQuR")
+ (synopsis "Batch effects removal for microbiome data")
+ (description
+ "This package conducts batch effects removal from a taxa read count
+table by a conditional quantile regression method. The distributional
+attributes of microbiome data - zero-inflation and over-dispersion, are
+simultaneously considered.")
+ (license license:gpl3))))
+
+(define-public r-p2data
+ (let ((commit "7d4c0e17d7899f9d9b08ab2bf455abe150912f4c")
+ (revision "1"))
+ (package
+ (name "r-p2data")
+ (version (git-version "1.0.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/kharchenkolab/p2data")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1hadrldldxvhqs43aqs3c88bqfgql3wcfkbll3jz7fh6z7p3x324"))))
+ (properties `((upstream-name . "p2data")))
+ (build-system r-build-system)
+ (home-page "https://github.com/kharchenkolab/p2data")
+ (synopsis "Data for pagoda2")
+ (description "This package contains data used by pagoda2. The data
+within this package are the 3000 bone marrow cells used for vignettes.")
+ (license license:gpl3))))
+
(define-public r-rhtslib12
(let ((commit "ee186daf04876969c7f31c16a0e0fda8e7c16a30")
(revision "1"))
@@ -747,6 +868,57 @@ high-throughput sequence analysis. The package is primarily useful to
developers of other R packages who wish to make use of HTSlib.")
(license license:lgpl2.0+))))
+(define-public r-stringendo
+ (let ((commit "83b8f2d82a09b33b9e895438bb523a021138be01")
+ (revision "1"))
+ (package
+ (name "r-stringendo")
+ (version (git-version "0.3.4" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vertesy/Stringendo")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1ap0nhbyd6xx0yl2vgmwk38p22yrkv4k9hw13r35z4wf343rry6v"))))
+ (properties `((upstream-name . "Stringendo")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-devtools r-usethis))
+ (home-page "https://github.com/vertesy/Stringendo")
+ (synopsis "Stringendo is a string parsing library")
+ (description
+ "This package provides string parsing functionalites for generating
+plotnames, filenames and paths.")
+ (license license:gpl3))))
+
+(define-public r-readwriter
+ (let ((commit "71454f4aa706f5d2fbe606acd95abc14224e7058")
+ (revision "1"))
+ (package
+ (name "r-readwriter")
+ (version (git-version "0.2.9" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vertesy/ReadWriter")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0sp27smhdva2hi2x0svia2l56k8xrh7p5akn78g5b0lcvz4x3hd7"))))
+ (properties `((upstream-name . "ReadWriter")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-gdata r-gtools r-openxlsx r-readr r-stringendo))
+ (home-page "https://github.com/vertesy/ReadWriter")
+ (synopsis "Functions to read and write files conveniently")
+ (description
+ "ReadWriter is a set of R functions to read and write files
+conveniently.")
+ (license license:gpl3))))
+
(define-public r-streamgraph
(let ((commit "76f7173ec89d456ace5943a512e20b1f6810bbcb")
(revision "1"))
@@ -1178,6 +1350,53 @@ It is the demultiplexing module of Pegasus, which is used by Cumulus in the
demultiplexing step.")
(license license:bsd-3)))
+(define-public python-doubletdetection
+ (package
+ (name "python-doubletdetection")
+ (version "4.2")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "doubletdetection" version))
+ (sha256
+ (base32
+ "0v0a19014h4p6x8pyz1s78xn3q5w5166cysvg574z6vw79a3s9vp"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:tests? #false ;there are none
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'use-poetry-core
+ (lambda _
+ ;; Patch to use the core poetry API.
+ (substitute* "pyproject.toml"
+ (("poetry.masonry.api")
+ "poetry.core.masonry.api")))))))
+ (propagated-inputs
+ (list python-anndata
+ python-ipywidgets
+ python-leidenalg
+ python-vtraag-louvain
+ python-matplotlib
+ python-numpy
+ python-pandas
+ python-phenograph
+ python-scanpy
+ python-scipy
+ python-tqdm))
+ (native-inputs
+ (list python-black
+ python-flake8
+ python-poetry-core
+ python-pytest))
+ (home-page "https://github.com/JonathanShor/DoubletDetection")
+ (synopsis
+ "This is a package to detect doublets in single-cell RNA-seq count matrices")
+ (description
+ "This package provides a method to detect and enable removal of doublets
+from single-cell RNA-sequencing.")
+ (license license:expat)))
+
(define-public python-hclust2
(package
(name "python-hclust2")
@@ -1255,6 +1474,66 @@ servers supporting the protocol.")
genomics data.")
(license license:bsd-3)))
+(define-public python-phenograph
+ (package
+ (name "python-phenograph")
+ (version "1.5.7")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "PhenoGraph" version))
+ (sha256
+ (base32
+ "0nji449mzwgp1f87iknl5fmnjdkrhkfkapxvafxdw01s0jg8zcj6"))
+ (modules '((guix build utils)))
+ ;; Remove bundled binaries
+ (snippet
+ '(delete-file-recursively "phenograph/louvain"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; This test can never succeed because Q_leiden is never set to
+ ;; anything other than None.
+ (add-after 'unpack 'disable-leiden-test
+ (lambda _
+ (substitute* "tests/test_cluster.py"
+ (("def test_run_leiden") "def _test_run_leiden"))))
+ (add-after 'unpack 'patch-louvain
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "phenograph/core.py"
+ (("lpath = os.path.*")
+ (string-append "lpath = \""
+ (dirname (search-input-file inputs "/bin/community"))
+ "\"\n"))
+ (("linux-(community|hierarchy|convert)" _ thing) thing)
+ ;; Do not write binaries, because the unmodified "convert"
+ ;; from louvain only knows how to process plain text files.
+ (("with open\\(filename \\+ \".bin\", \"w\\+b\"\\) as f:")
+ "with open(filename + \".bin\", \"w+\") as f:")
+ (("f.writelines\\(\\[e for t in zip\\(ij, s\\) for e in t\\]\\)")
+ "for [src, dest], weight in zip(ij, s): \
+f.write(src.astype(\"str\") + ' ' + \
+dest.astype(\"str\") + ' ' + \
+weight.astype(\"str\") + '\\n')")))))))
+ (inputs
+ (list louvain))
+ (propagated-inputs
+ (list python-leidenalg
+ python-numpy
+ python-psutil
+ python-scikit-learn
+ python-scipy))
+ (native-inputs
+ (list python-pytest))
+ (home-page "https://github.com/dpeerlab/PhenoGraph.git")
+ (synopsis "Graph-based clustering for high-dimensional single-cell data")
+ (description
+ "PhenoGraph is a clustering method designed for high-dimensional
+single-cell data. It works by creating a graph representing phenotypic
+similarities between cells and then identifying communities in this graph.")
+ (license license:expat)))
+
(define-public python-phylophlan
(package
(name "python-phylophlan")
@@ -1469,7 +1748,7 @@ use-case, we encourage users to compose functions to achieve their goals.")
python-scipy))
(native-inputs
(list python-cython python-pytest python-pytest-cov python-nose))
- (home-page "http://www.biom-format.org")
+ (home-page "https://www.biom-format.org")
(synopsis "Biological Observation Matrix (BIOM) format utilities")
(description
"The BIOM file format is designed to be a general-use format for
@@ -2396,7 +2675,7 @@ errors at the end of reads.")
("python" ,python-wrapper)))
(native-inputs
(list perl perl-clone perl-test-deep perl-test-simple))
- (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
+ (home-page "https://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
(synopsis "Fast and sensitive nucleotide sequence read aligner")
(description
"Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
@@ -2438,7 +2717,7 @@ gapped, local, and paired-end alignment modes.")
(inputs
(list python-wrapper tbb-2020 zlib))
(supported-systems '("x86_64-linux"))
- (home-page "http://bowtie-bio.sourceforge.net/index.shtml")
+ (home-page "https://bowtie-bio.sourceforge.net/index.shtml")
(synopsis "Fast aligner for short nucleotide sequence reads")
(description
"Bowtie is a fast, memory-efficient short read aligner. It aligns short
@@ -2559,7 +2838,7 @@ splice junctions between exons.")
;; Non-portable SSE instructions are used so building fails on platforms
;; other than x86_64.
(supported-systems '("x86_64-linux"))
- (home-page "http://bio-bwa.sourceforge.net/")
+ (home-page "https://bio-bwa.sourceforge.net/")
(synopsis "Burrows-Wheeler sequence aligner")
(description
"BWA is a software package for mapping low-divergent sequences against a
@@ -3152,7 +3431,7 @@ time.")
zlib))
(native-inputs
(list python-cython python-nose))
- (home-page "http://crossmap.sourceforge.net/")
+ (home-page "https://crossmap.sourceforge.net/")
(synopsis "Convert genome coordinates between assemblies")
(description
"CrossMap is a program for conversion of genome coordinates or annotation
@@ -3459,6 +3738,35 @@ and record oriented data modeling and the Semantic Web.")
resources for bioinformatics.")
(license license:bsd-3)))
+(define-public python-scrublet
+ (package
+ (name "python-scrublet")
+ (version "0.2.3")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "scrublet" version))
+ (sha256
+ (base32
+ "0fk5pwk12yz9wpvwkl6j2l2g28f3x35b9r9n5bw6f0i9f0qgd191"))))
+ (build-system pyproject-build-system)
+ (arguments '(#:tests? #false)) ;there are none
+ (propagated-inputs
+ (list python-annoy
+ python-cython
+ python-matplotlib
+ python-numba
+ python-numpy
+ python-pandas
+ python-scikit-image
+ python-scikit-learn
+ python-scipy
+ python-umap-learn))
+ (home-page "https://github.com/swolock/scrublet")
+ (synopsis "Tool to indentify and remove doublets in single-cell data")
+ (description "This package provides a tool for identifying and removing
+doublets in single-cell RNA-seq data.")
+ (license license:expat)))
+
(define-public cwltool
(package
(name "cwltool")
@@ -3663,6 +3971,80 @@ sequencing data. It uses paired-ends and split-reads to sensitively and
accurately delineate genomic rearrangements throughout the genome.")
(license license:gpl3+)))
+(define-public transanno
+ (package
+ (name "transanno")
+ (version "0.3.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/informationsea/transanno")
+ ;; Corresponds to tag v0.3.0
+ (commit "df49050c92644ea12d9d5c6fae2186ca436dbca3")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1jpn7s3cnd9ybk4lmfbhj2arhf6cmrv7jp74n7n87m3a3irkaif1"))
+ (snippet
+ '(with-output-to-file "liftover-rs/build.rs"
+ (lambda _
+ (format #true
+ "fn main() {~@
+ println!(\"cargo:rustc-link-lib=lzma\");~@
+ }~%"))))))
+ (build-system cargo-build-system)
+ (arguments
+ (list
+ #:install-source? #false ;fails
+ #:tests? #false ;"cargo test" ignores build.rs
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'prepare-test-files
+ (lambda _
+ (delete-file "Cargo.lock")
+ (substitute* "liftover-rs/Cargo.toml"
+ (("anyhow = \"1\"") "anyhow = \"1.0.65\""))
+ (substitute* "liftover-rs/prepare-test.sh"
+ (("/bin/bash")
+ (string-append #$(this-package-native-input "bash")
+ "/bin/bash")))
+ (invoke "bash" "prepare-test-files.sh")))
+ (add-before 'patch-cargo-checksums 'do-not-build-xz
+ (lambda _
+ ;; Detection of liblzma (in rust-lzma-sys, pulled in by
+ ;; rust-hts-sys) doesn't seem to work, or perhaps it really does
+ ;; request a static build somewhere.
+ (substitute* "guix-vendor/rust-lzma-sys-0.1.17.tar.xz/build.rs"
+ (("if .want_static && .msvc && pkg_config::probe_library\\(\"liblzma\"\\).is_ok\\(\\)") ""))))
+ (add-before 'install 'chdir
+ (lambda _ (chdir "transanno"))))
+ #:cargo-inputs
+ `(("rust-anyhow" ,rust-anyhow-1)
+ ("rust-autocompress" ,rust-autocompress-0.2)
+ ("rust-bio" ,rust-bio-0.41)
+ ("rust-clap" ,rust-clap-2)
+ ("rust-csv" ,rust-csv-1)
+ ("rust-flate2" ,rust-flate2-1)
+ ("rust-indexmap" ,rust-indexmap-1)
+ ("rust-log" ,rust-log-0.4)
+ ("rust-nom" ,rust-nom-5)
+ ("rust-once-cell" ,rust-once-cell-1)
+ ("rust-pretty-env-logger" ,rust-pretty-env-logger-0.3)
+ ("rust-regex" ,rust-regex-1)
+ ("rust-thiserror" ,rust-thiserror-1)
+ ("rust-serde" ,rust-serde-1)
+ ("rust-serde-json" ,rust-serde-json-1))
+ #:cargo-development-inputs
+ `(("rust-clap" ,rust-clap-2)
+ ("rust-lazy-static" ,rust-lazy-static-1))))
+ (native-inputs (list bash))
+ (home-page "https://github.com/informationsea/transanno")
+ (synopsis "LiftOver tool for new genome assemblies")
+ (description "This package provides an accurate VCF/GFF3/GTF LiftOver tool
+for new genome assemblies.")
+ (license license:gpl3+)))
+
(define-public trf
(package
(name "trf")
@@ -4747,7 +5129,7 @@ high-throughput sequencing (HTS) assays")
("java-xz" ,java-xz)))
(native-inputs
(list java-testng))
- (home-page "http://samtools.github.io/htsjdk/")
+ (home-page "https://samtools.github.io/htsjdk/")
(synopsis "Java API for high-throughput sequencing data (HTS) formats")
(description
"HTSJDK is an implementation of a unified Java library for accessing
@@ -4790,7 +5172,7 @@ manipulating HTS data.")
("java-xz" ,java-xz)))
(native-inputs
(list java-junit))
- (home-page "http://samtools.github.io/htsjdk/")
+ (home-page "https://samtools.github.io/htsjdk/")
(synopsis "Java API for high-throughput sequencing data (HTS) formats")
(description
"HTSJDK is an implementation of a unified Java library for accessing
@@ -4895,7 +5277,7 @@ manipulating HTS data.")
(list java-htsjdk java-guava))
(native-inputs
(list java-testng))
- (home-page "http://broadinstitute.github.io/picard/")
+ (home-page "https://broadinstitute.github.io/picard/")
(synopsis "Tools for manipulating high-throughput sequencing data and formats")
(description "Picard is a set of Java command line tools for manipulating
high-throughput sequencing (HTS) data and formats. Picard is implemented
@@ -4984,7 +5366,7 @@ Class-Path: /~a \
(list java-htsjdk-2.10.1))
(native-inputs
(list java-testng java-guava))
- (home-page "http://broadinstitute.github.io/picard/")
+ (home-page "https://broadinstitute.github.io/picard/")
(synopsis "Tools for manipulating high-throughput sequencing data and formats")
(description "Picard is a set of Java command line tools for manipulating
high-throughput sequencing (HTS) data and formats. Picard is implemented
@@ -5113,56 +5495,70 @@ VCF.")
(define-public fastqc
(package
(name "fastqc")
- (version "0.11.5")
+ (version "0.11.9")
(source
(origin
- (method url-fetch)
- (uri (string-append "http://www.bioinformatics.babraham.ac.uk/"
- "projects/fastqc/fastqc_v"
- version "_source.zip"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/s-andrews/FastQC")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "18rrlkhcrxvvvlapch4dpj6xc6mpayzys8qfppybi8jrpgx5cc5f"))))
+ "00y9drm0bkpxw8xfl8ysss18jmnhj8blgqgr6fpa58rkpfcbg8qk"))
+ (snippet
+ '(for-each delete-file
+ '("cisd-jhdf5.jar"
+ "sam-1.103.jar"
+ "jbzip2-0.9.jar")))))
(build-system ant-build-system)
(arguments
- `(#:tests? #f ; there are no tests
- #:build-target "build"
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'fix-dependencies
- (lambda* (#:key inputs #:allow-other-keys)
- (substitute* "build.xml"
- (("jbzip2-0.9.jar")
- (search-input-file inputs "/share/java/jbzip2.jar"))
- (("sam-1.103.jar")
- (search-input-file inputs
- "/share/java/sam-1.112.jar"))
- (("cisd-jhdf5.jar")
- (search-input-file inputs
- "/share/java/sis-jhdf5.jar")))))
- ;; There is no installation target
- (replace 'install
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin"))
- (share (string-append out "/share/fastqc/"))
- (exe (string-append share "/fastqc")))
- (for-each mkdir-p (list bin share))
- (copy-recursively "bin" share)
- (substitute* exe
- (("my \\$java_bin = 'java';")
- (string-append "my $java_bin = '"
- (assoc-ref inputs "java")
- "/bin/java';")))
- (chmod exe #o555)
- (symlink exe (string-append bin "/fastqc"))
- #t))))))
+ (list
+ #:tests? #f ;there are no tests
+ #:build-target "build"
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'fix-dependencies
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* '("build.xml" ".classpath")
+ (("jbzip2-0.9.jar")
+ (search-input-file inputs "/share/java/jbzip2.jar"))
+ (("sam-1.103.jar")
+ (search-input-file inputs "/share/java/sam-1.112.jar"))
+ (("cisd-jhdf5.jar")
+ (search-input-file inputs "/share/java/sis-jhdf5.jar")))))
+ ;; There is no installation target
+ (replace 'install
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let* ((bin (string-append #$output "/bin"))
+ (share (string-append #$output "/share/fastqc/"))
+ (exe (string-append share "/fastqc")))
+ (for-each mkdir-p (list bin share))
+ (copy-recursively "bin" share)
+ (substitute* exe
+ (("my \\$java_bin = \"java\";")
+ (string-append "my $java_bin = \""
+ ;; Use java from the JRE, not the JDK
+ #$(this-package-input "icedtea") "/bin/java"
+ "\";"))
+ (("\\$RealBin\\$delimiter\\$RealBin.*")
+ (string-append
+ (string-join
+ (list
+ share
+ (search-input-file inputs "/share/java/sam-1.112.jar")
+ (search-input-file inputs "/share/java/jbzip2.jar")
+ (search-input-file inputs "/share/java/sis-jhdf5.jar"))
+ "$delimiter")
+ "\";\n")))
+ (chmod exe #o555)
+ (symlink exe (string-append bin "/fastqc"))))))))
(inputs
- `(("java" ,icedtea)
- ("perl" ,perl) ; needed for the wrapper script
- ("java-cisd-jhdf5" ,java-cisd-jhdf5)
- ("java-picard-1.113" ,java-picard-1.113)
- ("java-jbzip2" ,java-jbzip2)))
+ (list icedtea
+ java-cisd-jhdf5
+ java-picard-1.113
+ java-jbzip2
+ perl)) ;needed for the wrapper script
(native-inputs
(list unzip))
(home-page "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/")
@@ -5190,7 +5586,7 @@ The main functions of FastQC are:
(define-public fastp
(package
(name "fastp")
- (version "0.20.1")
+ (version "0.23.2")
(source
(origin
(method git-fetch)
@@ -5200,20 +5596,21 @@ The main functions of FastQC are:
(file-name (git-file-name name version))
(sha256
(base32
- "0ly8mxdvrcy23jwxyppysx3dhb1lwsqhfbgpyvargxhfk6k700x4"))))
+ "04nmrqpjc3qni0cbazlwvpg8rk1mkfmfma0n4q3zivs3zi6rfnav"))))
(build-system gnu-build-system)
(arguments
- `(#:tests? #f ; there are none
- #:make-flags
- ,#~(list (string-append "PREFIX=" #$output))
- #: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")))))))
+ (list
+ #:tests? #false ;there are none
+ #:make-flags
+ #~(list (string-append "PREFIX=" #$output))
+ #:phases
+ #~(modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'install 'create-target-dir
+ (lambda _
+ (mkdir-p (string-append #$output "/bin")))))))
(inputs
- (list zlib))
+ (list isa-l libdeflate))
(home-page "https://github.com/OpenGene/fastp/")
(synopsis "All-in-one FastQ preprocessor")
(description
@@ -5404,21 +5801,22 @@ experiments and provide highly stable thresholds based on reproducibility.")
(outputs '("out" ;for library
"python")) ;for Python bindings
(arguments
- `(#:configure-flags
- ,#~(list "--without-sse" ; configure script probes for CPU features when SSE is enabled.
- (string-append "--enable-python-binding=" #$output:python))
- #:phases
- (modify-phases %standard-phases
+ (list
+ #:configure-flags
+ #~(list "--without-sse" ; configure script probes for CPU features when SSE is enabled.
+ (string-append "--enable-python-binding=" #$output:python))
+ #:phases
+ '(modify-phases %standard-phases
(add-before 'check 'set-SHELL-variable
(lambda _
;; generator_manager.hpp either uses /bin/sh or $SHELL
;; to run tests.
(setenv "SHELL" (which "bash")))))))
(native-inputs
- `(("bc" ,bc)
- ("time" ,time)
- ("python" ,python-wrapper)
- ("pkg-config" ,pkg-config)))
+ (list bc
+ time
+ python-wrapper
+ pkg-config))
(inputs
(list htslib))
(synopsis "Tool for fast counting of k-mers in DNA")
@@ -5567,7 +5965,7 @@ data.")
tar
wget
zlib))
- (home-page "http://kaiju.binf.ku.dk/")
+ (home-page "https://kaiju.binf.ku.dk/")
(synopsis "Fast and sensitive taxonomic classification for metagenomics")
(description "Kaiju is a program for sensitive taxonomic classification
of high-throughput sequencing reads from metagenomic whole genome sequencing
@@ -6083,7 +6481,7 @@ predicts the locations of structural units in the sequences.")
("openblas" ,openblas)))
(native-inputs
(list which))
- (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho")
+ (home-page "https://www.bioinf.uni-leipzig.de/Software/proteinortho")
(synopsis "Detect orthologous genes across species")
(description
"Proteinortho is a tool to detect orthologous genes across different
@@ -6358,7 +6756,7 @@ phylogenies.")
"rsem-run-prsem-testing-procedure"))))))))
(inputs
(list boost r-minimal perl htslib-1.3 zlib))
- (home-page "http://deweylab.biostat.wisc.edu/rsem/")
+ (home-page "https://deweylab.biostat.wisc.edu/rsem/")
(synopsis "Estimate gene expression levels from RNA-Seq data")
(description
"RSEM is a software package for estimating gene and isoform expression
@@ -6393,7 +6791,7 @@ BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
zlib))
(native-inputs
(list python-nose))
- (home-page "http://rseqc.sourceforge.net/")
+ (home-page "https://rseqc.sourceforge.net/")
(synopsis "RNA-seq quality control package")
(description
"RSeQC provides a number of modules that can comprehensively evaluate
@@ -6453,7 +6851,7 @@ distribution, coverage uniformity, strand specificity, etc.")
("readline" ,readline)))
(native-inputs
(list pkg-config))
- (home-page "http://seek.princeton.edu")
+ (home-page "https://seek.princeton.edu")
(synopsis "Gene co-expression search engine")
(description
"SEEK is a computational gene co-expression search engine. SEEK provides
@@ -6494,7 +6892,7 @@ to the user's query of interest.")
(native-inputs (list pkg-config))
(inputs
(list htslib ncurses perl python zlib))
- (home-page "http://samtools.sourceforge.net")
+ (home-page "https://samtools.sourceforge.net")
(synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
(description
"Samtools implements various utilities for post-processing nucleotide
@@ -7572,7 +7970,7 @@ optionally compressed by gzip.")
(install-file "SNAPCommand" bin)))))))
(native-inputs
(list zlib))
- (home-page "http://snap.cs.berkeley.edu/")
+ (home-page "https://snap.cs.berkeley.edu/")
(synopsis "Short read DNA sequence aligner")
(description
"SNAP is a fast and accurate aligner for short DNA reads. It is
@@ -7839,7 +8237,7 @@ sequences.")
;; no "configure" script
(delete 'configure))))
(inputs (list zlib))
- (home-page "http://subread.sourceforge.net/")
+ (home-page "https://subread.sourceforge.net/")
(synopsis "Tool kit for processing next-gen sequencing data")
(description
"The subread package contains the following tools: subread aligner, a
@@ -7886,7 +8284,7 @@ against local background noises.")
(install-file "stringtie" bin)))))))
(inputs
(list bzip2 htslib-for-stringtie libdeflate zlib))
- (home-page "http://ccb.jhu.edu/software/stringtie/")
+ (home-page "https://ccb.jhu.edu/software/stringtie/")
(synopsis "Transcript assembly and quantification for RNA-Seq data")
(description
"StringTie is a fast and efficient assembler of RNA-Seq sequence
@@ -8020,6 +8418,43 @@ sequence.")
(supported-systems '("i686-linux" "x86_64-linux"))
(license license:bsd-3)))
+(define-public r-ggexpress
+ (let ((commit "82f169385f87af328ff971195c2f64ff3c573a8a")
+ (revision "1"))
+ (package
+ (name "r-ggexpress")
+ (version (git-version "0.6.6" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vertesy/ggExpress")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "122hnw8xv33ngcd4fd7hmf817a06ih1knrxxi0cgklj1fwinm0z4"))))
+ (properties `((upstream-name . "ggExpress")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-cowplot
+ r-ggplot2
+ r-ggpubr
+ r-markdownhelpers
+ r-markdownreports
+ r-rcolorbrewer
+ r-sessioninfo
+ r-seurat
+ r-sm
+ r-stringendo
+ r-tidyverse))
+ (home-page "https://github.com/vertesy/ggExpress")
+ (synopsis
+ "This is a fast tool to create, annotate and export plots in R")
+ (description
+ "This package is a set of R functions for generating precise figures.
+This tool helps you to create clean markdown reports about what you just
+discovered with your analysis script.")
+ (license license:gpl3))))
+
(define-public r-gg3d
(let ((commit "ffdd837d30c1671cd0895db94bdd7b1594dbfcb0")
(revision "1"))
@@ -8336,7 +8771,10 @@ Pore-C concatemers.")
r-seurat
r-singlecellexperiment
r-slingshot
- r-summarizedexperiment))
+ r-summarizedexperiment
+ python
+ python-scrublet
+ python-doubletdetection))
(home-page "https://github.com/xnnba1984/DoubletCollection")
(synopsis "Tool for finding doublets in scRNA-seq data")
(description
@@ -8345,6 +8783,46 @@ doublet-detection methods. In addition, this tool is used for execution and
benchmark of those eight mentioned methods.")
(license license:gpl3+))))
+(define-public r-plsdabatch
+ (let ((commit "4aadf3a99709afae462db310386b6cf5db20088c")
+ (revision "1"))
+ (package
+ (name "r-plsdabatch")
+ (version (git-version "0.2.3" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/EvaYiwenWang/PLSDAbatch")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "047l923lq2ji7rwybh9b9zkblzvvhkpli5gb2x8g2q9f2n5022nr"))))
+ (properties `((upstream-name . "PLSDAbatch")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-ggplot2
+ r-ggpubr
+ r-gridextra
+ r-lmertest
+ r-mixomics
+ r-mvtnorm
+ r-performance
+ r-rdpack
+ r-scales))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/EvaYiwenWang/PLSDAbatch")
+ (synopsis "PLSDA-batch")
+ (description
+ "This package provides a new batch effect correction method based on
+Projection to Latent Structures Discriminant Analysis named “PLSDA-batch” to
+correct data prior to any downstream analysis. PLSDA-batch estimates latent
+components related to treatment and batch effects to remove batch variation.
+The method is multivariate, non-parametric and performs dimension reduction.
+Combined with centered log ratio transformation for addressing uneven library
+sizes and compositional structure, PLSDA-batch addresses all characteristics
+of microbiome data that existing correction methods have ignored so far.")
+ (license license:gpl3))))
+
(define-public r-psupertime
(let ((commit "73825a28d3bd9bc881c15ee0c4c218eec1c9c207")
(revision "1"))
@@ -8440,6 +8918,62 @@ target genes, Pando simultaneously infers gene modules and sets of regulatory
regions for each transcription factor.")
(license license:expat)))
+(define-public r-premessa
+ (let ((commit "68b42bb984637d0f3ad6a0ecc83e9278994afc85")
+ (revision "1"))
+ (package
+ (name "r-premessa")
+ (version (git-version "0.3.4" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ParkerICI/premessa")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1l0q431zk0lvg22130nx84gdqi7cpl05yah4am63lbx6m4c769pb"))
+ (snippet
+ '(delete-file "inst/normalizer_shinyGUI/www/d3.min.js"))))
+ (properties `((upstream-name . "premessa")))
+ (build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'process-javascript
+ (lambda* (#:key inputs #:allow-other-keys)
+ (with-directory-excursion "inst/normalizer_shinyGUI/www/"
+ (invoke "esbuild" (assoc-ref inputs "d3.v4.js")
+ "--minify" "--outfile=d3.min.js")))))))
+ (propagated-inputs
+ (list r-data-table
+ r-flowcore
+ r-ggplot2
+ r-gridextra
+ r-hexbin
+ r-jsonlite
+ r-reshape
+ r-rhandsontable
+ r-shiny
+ r-shinyjqui))
+ (native-inputs
+ `(("esbuild" ,esbuild)
+ ("d3.v4.js"
+ ,(origin
+ (method url-fetch)
+ (uri "https://d3js.org/d3.v4.js")
+ (sha256
+ (base32
+ "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
+ (home-page "https://github.com/ParkerICI/premessa")
+ (synopsis "Pre-processing of flow and mass cytometry data")
+ (description
+ "This is an R package for pre-processing of flow and mass cytometry
+data. This package includes panel editing or renaming for FCS files,
+bead-based normalization and debarcoding.")
+ (license license:gpl3))))
+
(define-public r-presto
(let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad")
(revision "0"))
@@ -8531,6 +9065,70 @@ auROC analysis.")
visualization and analysis of single-cell data using R.")
(license license:gpl3+))))
+(define-public r-markdownhelpers
+ (let ((commit "793372d28ebed607cc1d35f909a1caedb2b41ffe")
+ (revision "1"))
+ (package
+ (name "r-markdownhelpers")
+ (version (git-version "0.2.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vertesy/MarkdownHelpers")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1d18s2ydhfjm3hjkxz42dirhwrrv792m6mvkmypallaa2qnwrmkg"))))
+ (properties `((upstream-name . "MarkdownHelpers")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-devtools r-stringendo r-usethis))
+ (home-page "https://github.com/vertesy/MarkdownHelpers")
+ (synopsis "Helper functions for MarkdownReports and ggExpress")
+ (description
+ "This package provides a set of R functions to parse markdown and other
+generic helpers.")
+ (license license:gpl3))))
+
+(define-public r-markdownreports
+ (let ((commit "3ba1103e3ddc6df3a0c090eb884f5e65c461eb31")
+ (revision "1"))
+ (package
+ (name "r-markdownreports")
+ (version (git-version "4.5.9" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vertesy/MarkdownReports")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1xmasdb630b6nvxi5m1i8pyxiy49nxpzyxf9h8spdppx92rhdkc8"))))
+ (properties `((upstream-name . "MarkdownReports")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-clipr
+ r-codeandroll2
+ r-colorramps
+ r-devtools
+ r-gplots
+ r-markdownhelpers
+ r-rcolorbrewer
+ r-readwriter
+ r-sessioninfo
+ r-sm
+ r-stringendo
+ r-venndiagram
+ r-vioplot))
+ (home-page "https://github.com/vertesy/MarkdownReports")
+ (synopsis "Tool for generating cientific figures and reports")
+ (description
+ "This is a set of R functions that allows you to generate precise
+figures. This tool will create clean markdown reports about what you just
+discovered.")
+ (license license:gpl3))))
+
(define-public r-snapatac
(package
(name "r-snapatac")
@@ -8580,6 +9178,30 @@ clustering analysis, differential analysis, motif inference and exploration of
single cell ATAC-seq sequencing data.")
(license license:gpl3)))
+(define-public r-tictoc
+ (package
+ (name "r-tictoc")
+ (version "1.1")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "tictoc" version))
+ (sha256
+ (base32
+ "0ka7zd857xfqb5afn0psn0yzfv2qjb0ddxfyiq6aggbnla5qc3qj"))))
+ (properties `((upstream-name . "tictoc")))
+ (build-system r-build-system)
+ (home-page "https://github.com/jabiru/tictoc")
+ (synopsis
+ "Time R scripts and implementations of stack and list structures")
+ (description
+ "The tictoc package provides the timing functions @code{tic} and
+@code{toc} that can be nested. It provides an alternative to
+@code{system.time()} with a different syntax similar to that in another
+well-known software package. @code{tic} and @code{toc} are easy to use, and
+are especially useful when timing several sections in more than a few lines of
+code.")
+ (license license:asl2.0)))
+
(define-public r-tsis
(let ((commit "24460298fbe1d26e4da390f6e4f3d4d9d62334dc")
(revision "1"))
@@ -9000,7 +9622,7 @@ of contact distributions around selected landmarks.")
(base32
"1hsx6qgwr0i67fhy9257zj7s0ppncph2hjgbia5nn6nfmj0ax6l9"))))
(build-system r-build-system)
- (home-page "http://centipede.uchicago.edu/")
+ (home-page "https://centipede.uchicago.edu/")
(synopsis "Predict transcription factor binding sites")
(description
"CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions
@@ -9238,7 +9860,7 @@ experience substantial biological insertions and deletions.")
perl-getopt-long
perl-json
perl-statistics-pca))
- (home-page "http://prinseq.sourceforge.net/")
+ (home-page "https://prinseq.sourceforge.net/")
(synopsis "Preprocess sequence data in FASTA or FASTQ formats")
(description
"PRINSEQ is a bioinformatics tool to help you preprocess your genomic or
@@ -9723,7 +10345,7 @@ AM_CONDITIONAL(AMPNG, true)"))
zlib))
(native-inputs
(list autoconf automake libtool pkg-config))
- (home-page "http://emboss.sourceforge.net")
+ (home-page "https://emboss.sourceforge.net")
(synopsis "Molecular biology analysis suite")
(description "EMBOSS is the \"European Molecular Biology Open Software
Suite\". EMBOSS is an analysis package specially developed for the needs of
@@ -10400,7 +11022,7 @@ remove biased methylation positions for RRBS sequence files.")
(for-each (lambda (file)
(install-file file target))
(find-files "../exe" ".*"))))))))
- (home-page "http://evolution.genetics.washington.edu/phylip/")
+ (home-page "https://evolution.genetics.washington.edu/phylip/")
(synopsis "Tools for inferring phylogenies")
(description "PHYLIP (the PHYLogeny Inference Package) is a package of
programs for inferring phylogenies (evolutionary trees).")
@@ -14671,110 +15293,125 @@ datasets.")
(define-public ngless
(package
(name "ngless")
- (version "1.3.0")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/ngless-toolkit/ngless.git")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0pb9f6b0yk9p4cdwiym8r190q1bcdiwvc7i2s6rw54qgi8r3g6pj"))
- (patches (search-patches "ngless-unliftio.patch"))))
+ (version "1.5.0")
+ (source (origin
+ (method url-fetch)
+ (uri (hackage-uri "NGLess" version))
+ (sha256
+ (base32
+ "0pljyrlpr9r3cl5311dhgxdl8y40szyi4vprn34i3piy0qrldymi"))))
(build-system haskell-build-system)
(arguments
- (list
- #:haddock? #f ;The haddock phase fails with: NGLess/CmdArgs.hs:20:1:
- ;error: parse error on input import
- ;import Options.Applicative
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'create-Versions.hs
- (lambda _
- (substitute* "Makefile"
- (("BWA_VERSION = .*")
- (string-append "BWA_VERSION = "
- #$(package-version bwa) "\n"))
- (("SAM_VERSION = .*")
- (string-append "SAM_VERSION = "
- #$(package-version samtools) "\n"))
- (("PRODIGAL_VERSION = .*")
- (string-append "PRODIGAL_VERSION = "
- #$(package-version prodigal) "\n"))
- (("MINIMAP2_VERSION = .*")
- (string-append "MINIMAP2_VERSION = "
- #$(package-version minimap2) "\n")))
- (invoke "make" "NGLess/Dependencies/Versions.hs")))
- (add-after 'create-Versions.hs 'create-cabal-file
- (lambda _ (invoke "hpack")))
- ;; These tools are expected to be installed alongside ngless.
- (add-after 'install 'link-tools
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((bin (string-append #$output "/bin/")))
- (symlink (search-input-file inputs "/bin/prodigal")
- (string-append bin "ngless-" #$version "-prodigal"))
- (symlink (search-input-file inputs "/bin/minimap2")
- (string-append bin "ngless-" #$version "-minimap2"))
- (symlink (search-input-file inputs "/bin/samtools")
- (string-append bin "ngless-" #$version "-samtools"))
- (symlink (search-input-file inputs "/bin/bwa")
- (string-append bin "ngless-" #$version "-bwa"))))))))
- (inputs
- (list prodigal
- bwa
- samtools
- minimap2
- ghc-aeson
- ghc-ansi-terminal
- ghc-async
- ghc-atomic-write
- ghc-bytestring-lexing
- ghc-conduit
- ghc-conduit-algorithms
- ghc-conduit-extra
- ghc-configurator
- ghc-convertible
- ghc-data-default
- ghc-diagrams-core
- ghc-diagrams-lib
- ghc-diagrams-svg
- ghc-double-conversion
- ghc-edit-distance
- ghc-either
- ghc-errors
- ghc-extra
- ghc-filemanip
- ghc-file-embed
- ghc-gitrev
- ghc-hashtables
- ghc-http-conduit
- ghc-inline-c
- ghc-inline-c-cpp
- ghc-int-interval-map
- ghc-missingh
- ghc-optparse-applicative
- ghc-regex
- ghc-safe
- ghc-safeio
- ghc-strict
- ghc-tar
- ghc-tar-conduit
- ghc-unliftio
- ghc-unliftio-core
- ghc-vector
- ghc-yaml
- ghc-zlib))
+ `(#:haddock? #f
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'configure 'update-constraints
+ (lambda _
+ (substitute* "NGLess.cabal"
+ (("\\b(base)\\s+[^,]+" all dep)
+ dep))))
+ (add-after 'unpack 'create-Versions.hs
+ (lambda _
+ (substitute* "NGLess/Dependencies/Versions.hs"
+ (("bwaVersion = .+")
+ (string-append "bwaVersion = \""
+ ,(package-version bwa) "\""))
+ (("samtoolsVersion = .+")
+ (string-append "samtoolsVersion = \""
+ ,(package-version samtools) "\""))
+ (("prodigalVersion = .+")
+ (string-append "prodigalVersion = \""
+ ,(package-version prodigal) "\""))
+ (("megahitVersion = .+")
+ (string-append "megahitVersion = \""
+ ,(package-version megahit) "\""))
+ (("minimap2Version = .+")
+ (string-append "minimap2Version = \""
+ ,(package-version minimap2) "\"")))))
+ ;; See NGLess/FileManagement.hs.
+ (add-after 'install 'wrap-program
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bwa (search-input-file inputs "/bin/bwa"))
+ (samtools (search-input-file inputs "/bin/samtools"))
+ (prodigal (search-input-file inputs "/bin/prodigal"))
+ (minimap2 (search-input-file inputs "/bin/minimap2"))
+ (megahit (search-input-file inputs "/bin/megahit")))
+ (wrap-program (string-append out "/bin/ngless")
+ `("NGLESS_BWA_BIN" " " = (,bwa))
+ `("NGLESS_SAMTOOLS_BIN" " " = (,samtools))
+ `("NGLESS_PRODIGAL_BIN" " " = (,prodigal))
+ `("NGLESS_MINIMAP2_BIN" " " = (,minimap2))
+ `("NGLESS_MEGAHIT_BIN" " " = (,megahit))))))
+ ;; Sanity check.
+ (add-after 'wrap-program 'check-install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((ngless (string-append (assoc-ref outputs "out") "/bin/ngless")))
+ (invoke ngless "--check-install"))))
+ (add-after 'register 'remove-libraries
+ (lambda* (#:key outputs #:allow-other-keys)
+ (delete-file-recursively (string-append (assoc-ref outputs "out") "/lib")))))))
+ (inputs (list prodigal
+ bwa
+ samtools
+ minimap2
+ megahit
+ ghc-missingh
+ ghc-aeson
+ ghc-ansi-terminal
+ ghc-async
+ ghc-atomic-write
+ ghc-bytestring-lexing
+ ghc-conduit
+ ghc-conduit-algorithms
+ ghc-conduit-extra
+ ghc-configurator
+ ghc-convertible
+ ghc-data-default
+ ghc-edit-distance
+ ghc-either
+ ghc-errors
+ ghc-extra
+ ghc-file-embed
+ ghc-filemanip
+ ghc-hashable
+ ghc-hashtables
+ ghc-hostname
+ ghc-http-client
+ ghc-http-conduit
+ ghc-inline-c
+ ghc-inline-c-cpp
+ ghc-int-interval-map
+ ghc-network
+ ghc-optparse-applicative
+ ghc-primitive
+ ghc-random-shuffle
+ ghc-regex
+ ghc-resourcet
+ ghc-safe
+ ghc-stm-chans
+ ghc-stm-conduit
+ ghc-strict
+ ghc-tar
+ ghc-tar-conduit
+ ghc-unix-compat
+ ghc-unliftio
+ ghc-unliftio-core
+ ghc-vector
+ ghc-vector-algorithms
+ ghc-yaml
+ ghc-zlib
+ ghc-bzlib-conduit
+ ghc-double-conversion
+ ghc-safeio))
(propagated-inputs
(list r-r6 r-hdf5r r-iterators r-itertools r-matrix))
- (native-inputs
- (list ghc-hpack
- ghc-quickcheck
- ghc-test-framework
- ghc-test-framework-hunit
- ghc-test-framework-quickcheck2
- ghc-test-framework-th))
+ (native-inputs (list ghc-hunit
+ ghc-quickcheck
+ ghc-tasty
+ ghc-tasty-hunit
+ ghc-tasty-quickcheck
+ ghc-tasty-th))
(home-page "https://ngless.embl.de/")
(synopsis "DSL for processing next-generation sequencing data")
(description "Ngless is a domain-specific language for
@@ -15515,6 +16152,60 @@ information... The package can also be used to extract data from @code{.loom}
files.")
(license license:expat))))
+(define-public r-seurat-utils
+ (let ((commit "0b6f5b548a49148cfbeaa654e8a618c0a020afa5")
+ (revision "1"))
+ (package
+ (name "r-seurat-utils")
+ (version (git-version "1.6.5" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vertesy/Seurat.utils")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1mn64h375mkj6x4ix5493z32gqg96yc507j5jr0lx9g5wk1bf762"))))
+ (properties `((upstream-name . "Seurat.utils")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-codeandroll2
+ r-cowplot
+ r-dplyr
+ r-ggcorrplot
+ r-ggexpress
+ r-ggplot2
+ r-ggpubr
+ r-ggrepel
+ r-hgnchelper
+ r-htmlwidgets
+ r-markdownhelpers
+ r-markdownreports
+ r-matrix
+ r-matrixstats
+ r-princurve
+ r-r-utils
+ r-readr
+ r-readwriter
+ r-reshape2
+ r-scales
+ r-seurat
+ r-soupx
+ r-sparsematrixstats
+ r-stringendo
+ r-stringr
+ r-tibble
+ r-tictoc
+ r-vroom))
+ (home-page "https://github.com/vertesy/Seurat.utils")
+ (synopsis "Collection of utility functions for Seurat")
+ (description
+ "This is a collection of utility functions for Seurat. These functions
+allow the automation and multiplexing of plotting, 3D plotting, visualization
+of statistics & QC, interaction with the Seurat object. Some functionalities
+require functions from CodeAndRoll and MarkdownReports libraries.")
+ (license license:gpl3))))
+
(define-public r-seuratwrappers
;; There are no releases or tags.
(let ((commit "d28512f804d5fe05e6d68900ca9221020d52cf1d")
@@ -16679,7 +17370,7 @@ The output is in SAM format.")
(list libxml2))
(native-inputs
(list check swig))
- (home-page "http://sbml.org/Software/libSBML")
+ (home-page "https://sbml.org/Software/libSBML")
(synopsis "Process SBML files and data streams")
(description "LibSBML is a library to help you read, write, manipulate,
translate, and validate SBML files and data streams. The @dfn{Systems Biology
@@ -16810,6 +17501,40 @@ sequencing (e.g. mapping or base/indel alignment uncertainty), which are
usually ignored by other methods or only used for filtering.")
(license license:expat)))
+(define-public louvain
+ (package
+ (name "louvain")
+ (version "0.2")
+ (source (origin
+ (method url-fetch)
+ (uri "mirror://sourceforge/louvain/louvain_latest.tar.gz")
+ (sha256
+ (base32
+ "0hqlv5jqc889nbv7j1bchrx4zhh69hgr2mqvfdygc7kwrywn22lb"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:tests? #false ;there are none
+ #:phases
+ #~(modify-phases %standard-phases
+ (delete 'configure)
+ (add-after 'unpack 'patch-includes
+ (lambda _
+ (substitute* "main_community.cpp"
+ (("using namespace std;" m)
+ (string-append "#include <unistd.h> /* for getpid */\n" m)))))
+ (replace 'install
+ (lambda _
+ (for-each
+ (lambda (exe)
+ (install-file exe (string-append #$output "/bin")))
+ '("convert" "community" "hierarchy")))))))
+ (home-page "https://sourceforge.net/projects/louvain/")
+ (synopsis "Multi-criteria community detection")
+ (description "This package offers a set of functions to use in order to
+compute communities on graphs weighted or unweighted.")
+ (license license:gpl3+)))
+
(define-public ivar
(package
(name "ivar")
@@ -17598,7 +18323,6 @@ aligner.")
(list python-black
python-flake8
python-hypothesis
- python-pre-commit
python-pytest
python-setuptools-scm
python-wheel))
@@ -17616,7 +18340,7 @@ populations.")
(define-public scregseg
(package
(name "scregseg")
- (version "0.1.1")
+ (version "0.1.3")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -17625,16 +18349,22 @@ populations.")
(file-name (git-file-name name version))
(sha256
(base32
- "1k8hllr5if6k2mm2zj391fv40sfc008cjm04l9vgfsdppb80i112"))
+ "07g2barywa1wi8mggbxkbxqjw1fzd0a0l9cjdbkx4s40imb1dbxb"))
(snippet
- #~(begin
- (use-modules ((guix build utils)))
- (delete-file "src/scregseg/_utils.c")))))
- (build-system python-build-system)
+ '(delete-file "src/scregseg/_utils.c"))))
+ (build-system pyproject-build-system)
(arguments
- `(#:tests? #false ; tests require network access
- #:phases
- (modify-phases %standard-phases
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ ;; Numba needs a writable dir to cache functions.
+ (add-before 'check 'set-numba-cache-dir
+ (lambda _
+ (setenv "NUMBA_CACHE_DIR" "/tmp")))
+ ;; Cython extensions have to be built before running the tests.
+ (add-before 'check 'build-extensions
+ (lambda _
+ (invoke "python" "setup.py" "build_ext" "--inplace")))
(add-after 'unpack 'do-not-fail-to-find-sklearn
(lambda _
;; XXX: I have no idea why it cannot seem to find sklearn.
@@ -18552,7 +19282,7 @@ useful for bioinformatic analysis.")
(define-public go-github-com-biogo-hts-bam
(package
(name "go-github-com-biogo-hts-bam")
- (version "1.4.3")
+ (version "1.4.4")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -18561,7 +19291,7 @@ useful for bioinformatic analysis.")
(file-name (git-file-name name version))
(sha256
(base32
- "013ga6ilc4m3hyfr3yyiva9g4vs81afhj73v2sy7r75b5zxw7lx1"))))
+ "1vkcqxyajghx5p5j7g2i376nbsxh8q2smk0smlv8mi34yr7hlw5b"))))
(build-system go-build-system)
(arguments
'(#:import-path "github.com/biogo/hts/bam"
generated by cgit v1.2.3 (git 2.46.0) at 2024-08-27 04:25:12 +0000