;;; Copyright © 2017, 2021, 2022 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
-;;; Copyright © 2018, 2019, 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2018, 2019, 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
#:use-module (gnu packages jupyter)
#:use-module (gnu packages libffi)
#:use-module (gnu packages linux)
+ #:use-module (gnu packages llvm)
#:use-module (gnu packages logging)
#:use-module (gnu packages lsof)
#:use-module (gnu packages machine-learning)
intended to behave exactly the same as the original BWK awk.")
(license license:x11)))
+(define-public python-cellbender
+ (package
+ (name "python-cellbender")
+ (version "0.2.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/broadinstitute/CellBender")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1zav2q8nnss80i25y06fccagkvrqsy7lpylsl4dxv4qkj8p4fnv3"))))
+ (build-system python-build-system)
+ (arguments
+ (list #:tests? #false)) ;there are none
+ (propagated-inputs
+ (list python-anndata
+ python-matplotlib
+ python-numpy
+ python-pandas
+ python-pyro-ppl
+ python-scikit-learn
+ python-scipy
+ python-sphinx
+ python-sphinx-argparse
+ python-sphinx-autodoc-typehints
+ python-sphinx-rtd-theme
+ python-sphinxcontrib-programoutput
+ python-tables))
+ (home-page "https://cellbender.rtfd.io/")
+ (synopsis "Eliminate technical artifacts from single-cell RNA-seq data")
+ (description
+ "CellBender is a software package for eliminating technical artifacts
+from high-throughput single-cell RNA sequencing (scRNA-seq) data.")
+ (license license:bsd-3)))
+
(define-public python-htsget
(package
(name "python-htsget")
(define-public python-pybedtools
(package
(name "python-pybedtools")
- (version "0.8.2")
+ (version "0.9.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "pybedtools" version))
(sha256
(base32
- "0wc7z8g8prgdx7n5chjva2fdq03wiwhqisjjxzkjg1j5k5ha7151"))))
+ "18rhzk08d3rpxhi5xh6pqg64x6v5q3daw6y3v54k85v4swncjrwj"))))
(build-system python-build-system)
(arguments
`(#:modules ((srfi srfi-26)
(home-page "https://pythonhosted.org/pybedtools/")
(synopsis "Python wrapper for BEDtools programs")
(description
- "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs,
+ "This package is a Python wrapper for Aaron Quinlan's BEDtools programs,
which are widely used for genomic interval manipulation or \"genome algebra\".
pybedtools extends BEDTools by offering feature-level manipulations from with
Python.")
- (license license:gpl2+)))
+ ;; pypi lists GPLv2 in the PKG-INFO and website, but was relicensed in
+ ;; version 0.9.0 and the LICENSE.txt is consistant with the source code.
+ ;;
+ ;; pybedtools/include/gzstream.cpp and pybedtools/include/gzstream.h are
+ ;; licensed lgpl2.1+
+ (license (list license:expat license:lgpl2.1+))))
(define-public python-biom-format
(package
(base32
"1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh"))))))
-(define-public python2-biopython
- (package-with-python2 python-biopython))
-
(define-public python-fastalite
(package
(name "python-fastalite")
;; Remove useless msbuild directory
(delete-file-recursively
"c++/src/build-system/project_tree_builder/msbuild")
- #t))))
+
+ ;; Build reproducibly.
+ ;; Do not record the kernel version
+ (substitute* "c++/src/build-system/configure"
+ (("kver=.*") "kver=\"\""))
+ ;; Do not generate random numbers.
+ (substitute* "c++/scripts/common/impl/define_random_macros.sh"
+ (("#define NCBI_RANDOM_VALUE_MAX 0xffffffffu" m)
+ (string-append m "
+#define NCBI_RANDOM_VALUE_0 2845495105u
+#define NCBI_RANDOM_VALUE_1 2158634051u
+#define NCBI_RANDOM_VALUE_2 4072202242u
+#define NCBI_RANDOM_VALUE_3 902228395u
+#define NCBI_RANDOM_VALUE_4 1353323915u
+#define NCBI_RANDOM_VALUE_5 574823513u
+#define NCBI_RANDOM_VALUE_6 4119501261u
+#define NCBI_RANDOM_VALUE_7 2477640938u
+#define NCBI_RANDOM_VALUE_8 2776595395u
+#define NCBI_RANDOM_VALUE_9 270550684u
+"))
+ (("cksum") "cksum >/dev/null"))))))
(build-system gnu-build-system)
(arguments
`(;; There are two(!) tests for this massive library, and both fail with
`(#:tests? #f ; there are no tests
#:phases
(modify-phases %standard-phases
+ (add-before 'build 'set-force-source-date
+ ;; for reproducible dates, texlive needs this to respect respect
+ ;; SOURCE_DATE_EPOCH
+ (lambda _
+ (setenv "FORCE_SOURCE_DATE" "1")))
(add-after 'unpack 'fix-latex-errors
(lambda _
(with-fluids ((%default-port-encoding #f))
(inputs
(list gsl openblas zlib))
(native-inputs
- `(("catch" ,catch-framework2-1)
+ `(("catch" ,catch2-1)
("perl" ,perl)
("shunit2" ,shunit2)
("which" ,which)))
(define-public htseq
(package
(name "htseq")
- (version "0.12.3")
+ (version "2.0.2")
+ ;; Sources on pypi do not include everything needed to run the tests.
(source (origin
- (method url-fetch)
- (uri (pypi-uri "HTSeq" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/htseq/htseq")
+ (commit (string-append "release_" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0pk41vkzxsbb5nv644325mh8akmz4zdply9r2s80dgg5b21pgp0b"))))
+ "1kbr4ydjjhizz6r5m3xd4f0wj7qnn8zs0vnzghhgaa0yhbya5r19"))))
(build-system python-build-system)
- (native-inputs
- (list python-cython))
- ;; Numpy needs to be propagated when htseq is used as a Python library.
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ ;; Avoid rebuilding the extension. Everything is built during the
+ ;; 'install phase anyway.
+ (delete 'build)
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "pytest" "-v")))))))
(propagated-inputs
- (list python-numpy))
- (inputs
- (list python-pysam python-matplotlib))
- (home-page "https://htseq.readthedocs.io/")
- (synopsis "Analysing high-throughput sequencing data with Python")
+ (list python-matplotlib
+ python-numpy
+ python-pysam))
+ (native-inputs
+ (list python-cython
+ python-pandas
+ python-pytest
+ python-scipy
+ swig))
+ (home-page "https://github.com/htseq")
+ (synopsis "Framework for analyzing high-throughput sequencing data")
(description
- "HTSeq is a Python package that provides infrastructure to process data
-from high-throughput sequencing assays.")
+ "This package provides a framework to process and analyze data from
+high-throughput sequencing (HTS) assays")
(license license:gpl3+)))
(define-public java-htsjdk
(define-public plink-ng
(package (inherit plink)
(name "plink-ng")
- (version "2.00a3-20220315")
+ (version "2.00a3.3")
(source
(origin
(method git-fetch)
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "19inr47jwddkjb9kfb14yxc7xb16c73lkhgxj9sncb0fsiskb4x8"))))
+ (base32 "0m8wkyvbgvcr5kzc284w8fbhpxwglh2c1xq0yc3yv00a53gs7rv0"))))
(build-system gnu-build-system)
(arguments
- `(#:make-flags
- ,#~(list "BLASFLAGS=-llapack -lopenblas"
- "CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1"
- "ZLIB=-lz"
- "BIN=plink prettify"
- (string-append "CC=" #$(cc-for-target))
- (string-append "PREFIX=" #$output)
- "DESTDIR=")
- #:phases
- (modify-phases %standard-phases
+ (list
+ #:tests? #false ;TEST_EXTRACT_CHR doesn't produce expected files
+ #:make-flags
+ #~(list "BLASFLAGS=-llapack -lopenblas"
+ "NO_SSE42=1"
+ "NO_AVX2=1"
+ "STATIC_ZSTD="
+ (string-append "CC=" #$(cc-for-target))
+ (string-append "PREFIX=" #$output)
+ "DESTDIR=")
+ #:phases
+ '(modify-phases %standard-phases
(add-after 'unpack 'chdir
- (lambda _ (chdir "1.9")))
- (delete 'configure) ; no "configure" script
+ (lambda _ (chdir "2.0/build_dynamic")))
+ (delete 'configure) ; no "configure" script
(replace 'check
(lambda* (#:key tests? inputs #:allow-other-keys)
(when tests?
- (symlink "plink" "plink19")
- (symlink (search-input-file inputs "/bin/plink") "plink107")
(setenv "PATH" (string-append (getcwd) ":" (getenv "PATH")))
- (with-directory-excursion "tests"
- ;; The model test fails because of a 0.0001 difference.
- (substitute* "tests.py"
- (("diff -q test1.model test2.model")
- "echo yes"))
- (invoke "bash" "test_setup.sh")
- (invoke "python3" "tests.py"))))))))
+ (with-directory-excursion "../Tests"
+ (substitute* "run_tests.sh"
+ (("^./run_tests" m)
+ (string-append (which "bash") " " m)))
+ (invoke "bash" "run_tests.sh")))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (install-file "plink2"
+ (string-append
+ (assoc-ref outputs "out") "/bin")))))))
(inputs
- (list lapack openblas zlib))
+ (list lapack openblas zlib `(,zstd "lib")))
(native-inputs
- (list diffutils plink python)) ; for tests
+ (list diffutils plink python simde)) ; for tests
(home-page "https://www.cog-genomics.org/plink/")
(license license:gpl3+)))
sequence itself can be retrieved from these databases.")
(license license:bsd-3)))
+(define-public python-taggd
+ (package
+ (name "python-taggd")
+ (version "0.3.6")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/SpatialTranscriptomicsResearch/taggd")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0j19ah81z7aqrdljah9hyarp91gvgbk63pz6fz3pdpksy1yqyi6k"))
+ (modules '((guix build utils)))
+ (snippet
+ '(for-each delete-file
+ (find-files "taggd" "\\.c$")))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'disable-broken-tests
+ (lambda _
+ (substitute* "tests/taggd_demultiplex_test.py"
+ (("def test_normal_bam_run")
+ "def _disabled_test_normal_bam_run")))))))
+ (propagated-inputs
+ (list python-numpy python-pysam python-setuptools))
+ (native-inputs
+ (list python-cython))
+ (home-page "https://github.com/SpatialTranscriptomicsResearch/taggd")
+ (synopsis "Genetic barcode demultiplexing")
+ (description "This package provides TagGD barcode demultiplexing utilities
+for Spatial Transcriptomics data.")
+ (license license:bsd-3)))
+
+(define-public stpipeline
+ (package
+ (name "stpipeline")
+ (version "1.8.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "stpipeline" version))
+ (sha256
+ (base32
+ "0har2g42fvaqpiz66lincy86aj1hvwzds26kxhxfamvyvv4721wk"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "requirements.txt"
+ (("argparse.*") "")))))))
+ (propagated-inputs
+ (list htseq
+ python-cython
+ python-invoke
+ python-numpy
+ python-pandas
+ python-pympler
+ python-pysam
+ python-regex
+ python-scikit-learn
+ python-scipy
+ python-seaborn
+ python-setuptools
+ python-sqlitedict
+ python-taggd
+ samtools
+ star))
+ (home-page "https://github.com/SpatialTranscriptomicsResearch/st_pipeline")
+ (synopsis "Pipeline for spatial mapping of unique transcripts")
+ (description
+ "This package provides an automated pipeline for spatial mapping of
+unique transcripts.")
+ (license license:expat)))
+
(define-public sra-tools
(package
(name "sra-tools")
(supported-systems '("i686-linux" "x86_64-linux"))
(license license:bsd-3)))
+(define-public r-gutils
+ (let ((commit "10e36c7b580aacb2d952140a3fdd82418aaddea6")
+ (revision "1"))
+ (package
+ (name "r-gutils")
+ (version (git-version "0.2.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mskilab/gUtils")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1wq9kd1afzy7ii510r20c4n9fkykj6p15q5c85ws27h1q5w4ghxy"))))
+ (properties `((upstream-name . "gUtils")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocgenerics
+ r-data-table
+ r-genomeinfodb
+ r-genomicranges
+ r-iranges
+ r-matrix
+ r-s4vectors
+ r-stringr))
+ (home-page "https://github.com/mskilab/gUtils")
+ (synopsis "Additional capabilities and speed for GenomicRanges operations")
+ (description
+ "This is an R package providing additional capabilities and speed for
+@code{GenomicRanges} operations.")
+ (license license:gpl2))))
+
+(define-public r-bamutils
+ (let ((commit "639dba901f16944fa1b7a8d7048701ba86a2cdb8")
+ (revision "1"))
+ (package
+ (name "r-bamutils")
+ (version (git-version "0.0.0.9000" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mskilab/bamutils/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0qwby2v5rydnipvf1iv1wz9nf02yq98k0xbc4inf9mqc54jwacs0"))))
+ (properties `((upstream-name . "bamUtils")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-abind
+ r-biocgenerics
+ r-data-table
+ r-genomicalignments
+ r-genomicranges
+ r-gutils
+ r-rsamtools
+ r-variantannotation))
+ (home-page "https://github.com/mskilab/bamutils/")
+ (synopsis "Utility functions for manipulating BAMs")
+ (description "This package provides utility functions for manipulating
+BAM files.")
+ (license license:gpl2))))
+
+(define-public r-gtrack
+ (let ((commit "a694fa36cedafca2658da79fc8e5b673535b15e5")
+ (revision "1"))
+ (package
+ (name "r-gtrack")
+ (version (git-version "0.1.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mskilab/gTrack/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "070qlrbqsbj9max2vx740zigqh0ymvnw2pm1ia5la3wb4dbfwh2b"))))
+ (properties `((upstream-name . "gTrack")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocgenerics
+ r-data-table
+ r-genomeinfodb
+ r-genomicranges
+ r-gutils
+ r-iranges
+ r-matrix
+ r-rcolorbrewer
+ r-rcpp
+ r-rcurl
+ r-rtracklayer
+ r-s4vectors))
+ (home-page "https://github.com/mskilab/gTrack/")
+ (synopsis "Plot tracks of complex genomic data across multiple genomic windows")
+ (description
+ "This package provides an object for plotting GRanges, RleList, UCSC
+file formats, and ffTrack objects in multi-track panels.")
+ (license license:gpl2))))
+
+(define-public r-gchain
+ (let ((commit "dc393e8dd0d8efaf36270c04d7112db8553db36a")
+ (revision "1"))
+ (package
+ (name "r-gchain")
+ (version (git-version "0.2.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mskilab/gChain/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "105wgi5w2fhwq1grsvj6zjigwg0sny3z7zr577q8ki3qffjwdkj0"))))
+ (properties `((upstream-name . "gChain")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-bamutils
+ r-biostrings
+ r-data-table
+ r-genomicalignments
+ r-genomicranges
+ r-gtrack
+ r-gutils
+ r-matrix
+ r-rtracklayer))
+ (home-page "https://github.com/mskilab/gChain/")
+ (synopsis "Additional capabilities and speed for GenomicRanges operations")
+ (description
+ "This R package provides additional capabilities and speed for
+GenomicRanges operations.")
+ (license license:gpl2))))
+
+(define-public r-skitools
+ (let ((commit "22d107d32f063eb891eb5e7fb36996d1c0b0d2bc")
+ (revision "1"))
+ (package
+ (name "r-skitools")
+ (version (git-version "0.0.0.9000" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mskilab/skitools/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1977d9bkdk9l2n6niahfj9vksh9l1ga4g7c3b3x27lj1gc0qgr4z"))))
+ (properties `((upstream-name . "skitools")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biostrings
+ r-complexheatmap
+ r-data-table
+ r-devtools
+ r-dt
+ r-gchain
+ r-genomeinfodb
+ r-genomicranges
+ r-ggplot2
+ r-gplots
+ r-gutils
+ r-htmlwidgets
+ r-hwriter
+ r-igraph
+ r-iranges
+ r-plotly
+ r-rcolorbrewer
+ r-reshape2
+ r-s4vectors
+ r-stringr
+ r-variantannotation))
+ (home-page "https://github.com/mskilab/skitools/")
+ (synopsis "Various mskilab R utilties")
+ (description
+ "This package provides R miscellaneous utilities for basic data
+manipulation, debugging, visualization, lsf management, and common mskilab
+tasks.")
+ (license license:expat))))
+
+(define-public r-chromunity
+ (let ((commit "09fce8bc12cb84b45a6ea25bf8db6e5b75113d4f")
+ (revision "1"))
+ (package
+ (name "r-chromunity")
+ (version (git-version "0.0.1" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mskilab/chromunity")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0lp0h614k8fq6h9gpbylk4chh7q6w4qda8lx03ajrpppxmg7al2d"))))
+ (properties `((upstream-name . "chromunity")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-arrow
+ r-biocgenerics
+ r-data-table
+ r-gchain
+ r-genomicranges
+ r-gutils
+ r-igraph
+ r-magrittr
+ r-mass
+ r-matrix
+ r-pbmcapply
+ r-plyr
+ r-r6
+ r-skitools
+ r-zoo))
+ (home-page "https://github.com/mskilab/chromunity")
+ (synopsis "Discovery of communities in Pore-C concatemers")
+ (description "This is a package for the discovery of communities in
+Pore-C concatemers.")
+ (license license:gpl3))))
+
(define-public r-presto
(let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad")
(revision "0"))
auROC analysis.")
(license license:gpl3))))
-(define-public r-snapatac
- (package
- (name "r-snapatac")
- (version "2.0")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/r3fang/SnapATAC")
+(define-public r-sccustomize
+ (let ((commit "8414d1f5fb32277855b0619191a568932b7baeb0")
+ (revision "1"))
+ (package
+ (name "r-sccustomize")
+ (version (git-version "0.7.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/samuel-marsh/scCustomize")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1wcgfq7lx83a2kf8pjbw524gdvxf351n08cwd5wzmmy57kf4knbj"))))
+ (properties `((upstream-name . "scCustomize")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-circlize
+ r-colorway
+ r-cowplot
+ r-data-table
+ r-dittoseq
+ r-dplyr
+ r-forcats
+ r-ggbeeswarm
+ r-ggplot2
+ r-ggprism
+ r-ggpubr
+ r-ggrastr
+ r-ggrepel
+ r-glue
+ r-janitor
+ r-magrittr
+ r-matrix
+ r-paletteer
+ r-patchwork
+ r-pbapply
+ r-purrr
+ r-remotes
+ r-scales
+ r-scattermore
+ r-seurat
+ r-seuratobject
+ r-stringi
+ r-stringr
+ r-tibble
+ r-tidyr
+ r-tidyselect
+ r-viridis))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/samuel-marsh/scCustomize")
+ (synopsis "Custom visualization and analyses of single-cell sequencing")
+ (description
+ "This is a collection of functions created and/or curated to aid in the
+visualization and analysis of single-cell data using R.")
+ (license license:gpl3+))))
+
+(define-public r-snapatac
+ (package
+ (name "r-snapatac")
+ (version "2.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/r3fang/SnapATAC")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
;; See https://github.com/hms-dbmi/scde/issues/38
(license license:gpl2)))
+(define-public r-millefy
+ (package
+ (name "r-millefy")
+ (version "0.1.9-beta")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/yuifu/millefy")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0z2y0x99f761pxvg6n37cmnyrnj699jhjk43pvk05sa86iykgizl"))))
+ (properties `((upstream-name . "millefy")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-data-table
+ r-destiny
+ r-dplyr
+ r-genomicranges
+ r-iranges
+ r-magrittr
+ r-rsamtools
+ r-rtracklayer
+ r-tidyr))
+ (home-page "https://github.com/yuifu/millefy")
+ (synopsis "Make millefy plot with single-cell RNA-seq data")
+ (description "@code{Millefy} is a tool for visualizing read coverage of
+@dfn{scRNA-seq}(single-cell RNA sequencing) datasets in genomic contexts. By
+dynamically and automatically reorder single cells based on locus-specific
+pseudo time, @code{Millefy} highlights cell-to-cell heterogeneity in read coverage
+of scRNA-seq data.")
+ (license license:expat)))
+
(define-public r-misha
(package
(name "r-misha")
;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+)
(license (list license:ruby license:lgpl2.1+ license:gpl2+ ))))
+(define-public centrifuge
+ (package
+ (name "centrifuge")
+ (version "1.0.4")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/DaehwanKimLab/centrifuge.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "167610gbz1rrh6ir3j7jcmhzg3x5msn7x7a3dpv7wmwdndnnqvg0"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:tests? #false ; no check target
+ #:make-flags
+ #~(list (string-append "prefix=" #$output))
+ #:phases
+ '(modify-phases %standard-phases
+ (delete 'configure))))
+ (inputs (list python-wrapper))
+ (native-inputs
+ (list pandoc perl ;for documentation
+ which))
+ (home-page "https://github.com/DaehwanKimLab/centrifuge/")
+ (synopsis "Classifier for metagenomic sequences")
+ (description "Centrifuge is a microbial classification engine that enables
+rapid, accurate and sensitive labeling of reads and quantification of species
+on desktop computers. The system uses an indexing scheme based on the
+@dfn{Burrows-Wheeler transform} (BWT) and the @dfn{Ferragina-Manzini} (FM)
+index, optimized specifically for the metagenomic classification problem.
+Centrifuge requires a relatively small index (4.7 GB for all complete
+bacterial and viral genomes plus the human genome) and classifies sequences at
+very high speed, allowing it to process the millions of reads from a typical
+high-throughput DNA sequencing run within a few minutes.")
+ (license license:gpl3+)))
+
(define-public bio-vcf
(package
(name "bio-vcf")
programs for inferring phylogenies (evolutionary trees).")
(license license:bsd-2)))
+(define-public phyml
+ (package
+ (name "phyml")
+ (version "3.3.20220408")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/stephaneguindon/phyml")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "03hdqmnsgnzkcrp9r9ajdfkj33jgq4b86kra8ssjlrph65y344sa"))
+ (snippet
+ '(delete-file "doc/phyml-manual.pdf"))))
+ (build-system gnu-build-system)
+ (supported-systems '("x86_64-linux"))
+ (arguments
+ (let ((default-flags (list "--disable-native")))
+ `(#:phases
+ (let ((build (lambda (what)
+ (lambda args
+ (apply (assoc-ref %standard-phases 'configure)
+ (append args
+ (list #:configure-flags
+ (cons (format #false "--enable-~a" what)
+ '() #;,default-flags))))
+ (apply (assoc-ref %standard-phases 'build) args)
+ (apply (assoc-ref %standard-phases 'install) args)))))
+ (modify-phases %standard-phases
+ ;; We cannot use --disable-native; see
+ ;; https://github.com/stephaneguindon/phyml/issues/173 Instead we
+ ;; patch the code to at least get rid of -march=native.
+ (add-after 'unpack 'remove-march-native
+ (lambda _
+ (substitute* "configure.ac"
+ (("DEFAULT_VECTOR_FLAG=\"-march=native\"")
+ "DEFAULT_VECTOR_FLAG=\"-march=athlon64-sse3\"\n"))))
+ (add-after 'build 'build-manual
+ (lambda _
+ (with-directory-excursion "doc"
+ (invoke "make" "phyml-manual.pdf"))))
+ (add-after 'build-manual 'install-manual
+ (lambda* (#:key outputs #:allow-other-keys)
+ (with-directory-excursion "doc"
+ (install-file "phyml-manual.pdf"
+ (string-append (assoc-ref outputs "out")
+ "/share/doc/phyml")))))
+ (add-after 'install 'build-phyml-mpi
+ (build "phyml-mpi"))
+ (add-after 'build-phyml-mpi 'build-rf
+ (build "rf"))
+ (add-after 'build-rf 'build-phyrex
+ (build "phyrex")))))))
+ (native-inputs
+ (list automake
+ autoconf
+ openmpi
+ (texlive-updmap.cfg (list texlive-amsfonts
+ texlive-caption
+ texlive-cite
+ texlive-fonts-ec
+ texlive-grfext
+ texlive-hyperref
+ texlive-latex-fancyvrb
+ texlive-latex-graphics
+ texlive-latex-psfrag
+ texlive-xcolor))))
+ (home-page "https://github.com/stephaneguindon/phyml")
+ (synopsis "Programs for working on SAM/BAM files")
+ (description
+ "@code{PhyML} is a software package that uses modern statistical
+approaches to analyse alignments of nucleotide or amino acid sequences in a
+phylogenetic framework. The main tool in this package builds phylogenies
+under the maximum likelihood criterion. It implements a large number of
+substitution models coupled with efficient options to search the space of
+phylogenetic tree topologies. code{PhyREX} fits the
+spatial-Lambda-Fleming-Viot model to geo-referenced genetic data. This model
+is similar to the structured coalescent but assumes that individuals are
+distributed along a spatial continuum rather than discrete demes.
+@code{PhyREX} can be used to estimate population densities and rates of
+dispersal. Its output can be processed by treeannotator (from the
+@code{BEAST} package) as well as @code{SPREAD}.")
+ (license license:gpl3)))
+
(define-public imp
(package
(name "imp")
(inputs
`(("boost" ,boost)
("bzip2" ,bzip2)
- ("cereal" ,cereal)
+ ("cereal" ,cereal-1.3.0)
("curl" ,curl)
("eigen" ,eigen)
("jemalloc" ,jemalloc)
(define-public pigx-rnaseq
(package
(name "pigx-rnaseq")
- (version "0.0.20")
+ (version "0.1.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
"/pigx_rnaseq-" version ".tar.gz"))
(sha256
(base32
- "0bf65qqvlkc77vl7cmmzacq70f0qav4p6nf8pp3x1vdd0nvhr24f"))))
+ "0acdjimfb9ywba8zsv7lavv436pmcmp8ra683h11wr4s3681pqk8"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-tests? #f ; not supported
(define-public pigx-chipseq
(package
(name "pigx-chipseq")
- (version "0.0.53")
+ (version "0.1.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
"/pigx_chipseq-" version ".tar.gz"))
(sha256
(base32
- "0c6npx35sszycf059w1x1k4k9hq1qqxny0i4p57q1188czr4561h"))
- (patches (search-patches "pigx-chipseq-no-citeproc.patch"))))
+ "008n6drj9q5av86xihxlj4py2c9p3c5z5ld89c3bksrp77zxiy67"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; parts of the tests rely on access to the network
#:phases
(modify-phases %standard-phases
- (add-before 'bootstrap 'autoreconf
- (lambda _
- ;; This was fixed in commit
- ;; 0b1c9f7f2e4d0ff601f1de95ab8b2953f4d5dbc7, but there is no
- ;; release with this fix.
- (call-with-output-file "VERSION"
- (lambda (port) (display ,version port)))
- ;; See https://github.com/BIMSBbioinfo/pigx_chipseq/issues/176
- (substitute* "m4/ax_r_package.m4"
- (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)")
- "if(system.file(package=\"PKG\") == \"\")"))
- (invoke "autoreconf" "-vif")))
(add-before 'configure 'set-PYTHONPATH
(lambda _
(setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))))))
bedtools
kentutils))
(native-inputs
- (list autoconf automake python-pytest))
+ (list 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
(define-public pigx-bsseq
(package
(name "pigx-bsseq")
- (version "0.1.6")
+ (version "0.1.8")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
"/pigx_bsseq-" version ".tar.gz"))
(sha256
(base32
- "1dipikph0xdr8fp0h1flpafcrg60y4aabljg8fl1v92j3gxdggmw"))
- (patches (search-patches "pigx-bsseq-no-citeproc.patch"))))
+ "1s8zgrqxabrawrgkga5rmgb0gyzj7ck47p3rkicjkfv7r2yjy0d7"))))
(build-system gnu-build-system)
(arguments
`(;; TODO: tests currently require 12+GB of RAM. See
#:tests? #f
#:phases
(modify-phases %standard-phases
- (add-before 'bootstrap 'autoreconf
- (lambda _
- ;; This was fixed in commit
- ;; d56ac732524da659afbbb0972f7a87fa178ae58e, but there is no
- ;; release with this fix.
- (call-with-output-file "VERSION"
- (lambda (port) (display ,version port)))
- ;; https://github.com/BIMSBbioinfo/pigx_bsseq/issues/181
- (substitute* "m4/ax_r_package.m4"
- (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)")
- "if(system.file(package=\"PKG\") == \"\")"))
- (invoke "autoreconf" "-vif")))
(add-before 'configure 'set-PYTHONPATH
(lambda _
(setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))
(search-input-directory inputs
"share/zoneinfo")))))))
(native-inputs
- (list tzdata automake autoconf))
+ (list tzdata))
(inputs
(list coreutils
sed
(define-public pigx-scrnaseq
(package
(name "pigx-scrnaseq")
- (version "1.1.8")
+ (version "1.1.9")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
"/pigx_scrnaseq-" version ".tar.gz"))
(sha256
(base32
- "1lc42hl8mz95kilh0z39s3wnv092mhm6vl2i394n0yfvdzk4f885"))))
+ "0adx7877c3lhlrzfid76i8bc829wcmzvrm0jx47gyid8mxqb7vqs"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
- (add-before 'bootstrap 'autoreconf
- (lambda _
- ;; This was fixed in commit
- ;; c4ac067438ae9312b5786a72e2bfb3d795e3ec8a, but there is no
- ;; release with this fix.
- (call-with-output-file "VERSION"
- (lambda (port) (display ,version port)))
- ;; https://github.com/BIMSBbioinfo/pigx_scrnaseq/issues/59
- (substitute* "m4/ax_r_package.m4"
- (("if\\(is.na\\(packageDescription\\(\"PKG\"\\)\\)\\)")
- "if(system.file(package=\"PKG\") == \"\")"))
- (invoke "autoreconf" "-vif")))
(add-before 'configure 'set-additional-environment-variables
(lambda _
;; Needed because of loompy
r-singlecellexperiment
r-stringr
r-yaml))
- (native-inputs
- (list autoconf automake))
(home-page "https://bioinformatics.mdc-berlin.de/pigx/")
(synopsis "Analysis pipeline for single-cell RNA sequencing experiments")
(description
(define-public python-mappy
(package
(name "python-mappy")
- (version "2.18")
+ (version "2.24")
(source (origin
(method url-fetch)
(uri (pypi-uri "mappy" version))
(sha256
(base32
- "1a05p7rkmxa6qhm108na8flzj2v45jab06drk59kzk1ip2sgvzqq"))))
+ "1ycszza87p9qvx8mis9v1hry0ac465x1xcxbsn1k45qlxxrzp8im"))))
(build-system python-build-system)
(native-inputs
(list python-cython))
(install-file "Bandage" (string-append out "/bin"))
#t))))))
(inputs
- (list qtbase-5 qtsvg))
+ (list qtbase-5 qtsvg-5))
(native-inputs
(list imagemagick))
(home-page "https://rrwick.github.io/Bandage/")
(license license:gpl3+)))
(define-public r-dyngen
- (let ((commit "37fd1798fcbd41093fb3d7775bb2d268e2fc82b6")
+ (package
+ (name "r-dyngen")
+ (version "1.0.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "dyngen" version))
+ (sha256
+ (base32
+ "1qmqy0dyiz30zpf3ii4h2ip6hg2449ghb474sjzrqa1yk9mdpy4i"))))
+ (properties `((upstream-name . "dyngen")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-assertthat
+ r-dplyr
+ r-dynutils
+ r-ggplot2
+ r-ggraph
+ r-ggrepel
+ r-gillespiessa2
+ r-igraph
+ r-lmds
+ r-matrix
+ r-patchwork
+ r-pbapply
+ r-purrr
+ r-rlang
+ r-tibble
+ r-tidygraph
+ r-tidyr
+ r-viridis))
+ (home-page "https://github.com/dynverse/dyngen")
+ (synopsis "Multi-Modal simulator for single-cell omics analyses")
+ (description
+ "This package provides a multi-modal simulation engine for studying
+dynamic cellular processes at single-cell resolution.")
+ (license license:expat)))
+
+;; Needed for r-liana
+(define-public r-omnipathr/devel
+ (let ((commit "679bb79e319af246a16968d27d64d8d6937a331a")
(revision "1"))
(package
- (name "r-dyngen")
- (version (git-version "1.0.3" revision commit))
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/dynverse/dyngen")
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32 "05pr6v1b8yji1jnj3fwx0crmg8ay6yy6lp9qjmcyvhkwbmf3kvc7"))))
- (properties `((upstream-name . "dyngen")))
+ (name "r-omnipathr")
+ (version (git-version "3.5.5" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/saezlab/omnipathr")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "10h6lyapyx4ik8r4kx5z2dly46jlf2v57caq4g6i0hzifyz2vgjq"))))
+ (properties `((upstream-name . "OmnipathR")))
(build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'set-HOME
+ (lambda _ (setenv "HOME" "/tmp"))))))
(propagated-inputs
- (list r-assertthat
+ (list r-checkmate
+ r-crayon
+ r-curl
+ r-digest
r-dplyr
- r-dynutils
- r-ggplot2
- r-ggraph
- r-ggrepel
- r-gillespiessa2
+ r-httr
r-igraph
- r-lmds
- r-matrix
- r-patchwork
- r-pbapply
+ r-jsonlite
+ r-later
+ r-logger
+ r-magrittr
+ r-progress
r-purrr
+ r-rappdirs
+ r-readr
+ r-readxl
r-rlang
+ r-rvest
+ r-stringr
r-tibble
- r-tidygraph
r-tidyr
- r-viridis))
- (home-page "https://github.com/dynverse/dyngen")
- (synopsis "Multi-Modal simulator for single-cell omics analyses")
+ r-tidyselect
+ r-withr
+ r-xml2
+ r-yaml))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/saezlab/omnipathr")
+ (synopsis "OmniPath web service client and more")
(description
- "This package provides a multi-modal simulation engine for studying
-dynamic cellular processes at single-cell resolution.")
+ "This package provides a client for the OmniPath web service and many
+other resources. It also includes functions to transform and pretty print
+some of the downloaded data, functions to access a number of other resources
+such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to
+Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology,
+InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015,
+RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore,
+OmnipathR features a close integration with the NicheNet method for ligand
+activity prediction from transcriptomics data, and its R implementation
+@code{nichenetr}.")
(license license:expat))))
+(define-public r-liana
+ (let ((commit "efb1249af46f576d1d620956053cfa93b2cee961")
+ (revision "1"))
+ (package
+ (name "r-liana")
+ (version (git-version "0.1.5" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/saezlab/liana/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0z645k26kqrfj5f1s412vwclw1q47h1zfxxrh9ijr30pxhpv6cv0"))))
+ (properties `((upstream-name . "liana")))
+ (build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ `(modify-phases %standard-phases
+ ;; This is needed to find ~/.config/OmnipathR/omnipathr.yml
+ (add-after 'unpack 'set-HOME
+ (lambda _ (setenv "HOME" "/tmp"))))))
+ (propagated-inputs
+ (list r-complexheatmap
+ r-dplyr
+ r-ggplot2
+ r-magrittr
+ r-omnipathr/devel
+ r-purrr
+ r-rcolorbrewer
+ r-readr
+ r-reticulate
+ r-rlang
+ r-scater
+ r-scran
+ r-scuttle
+ r-seuratobject
+ r-singlecellexperiment
+ r-stringr
+ r-tibble
+ r-tidyr
+ r-tidyselect))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/saezlab/liana/")
+ (synopsis "LIANA: a LIgand-receptor ANalysis frAmework")
+ (description
+ "LIANA provides a number of methods and resource for ligand-receptor
+interaction inference from scRNA-seq data.")
+ (license license:gpl3))))
+
(define-public r-circus
(package
(name "r-circus")
(define-public python-bbknn
(package
(name "python-bbknn")
- (version "1.3.6")
+ (version "1.5.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "bbknn" version))
(sha256
(base32
- "1jbsh01f57zj4bhvjr3jh4532zznqd6nccmgrl3qi9gnhkf7c4y0"))))
+ "0q11xdmjr2kf6f179a6kjizj3lllfrq743gslgw67qyzimvrrnhn"))))
(build-system python-build-system)
(arguments
`(#:tests? #f ; no tests are included
#: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")))
(add-after 'unpack 'do-not-fail-to-find-sklearn
(lambda _
;; XXX: I have no idea why it cannot seem to find sklearn.
(list python-annoy
python-cython
python-numpy
+ python-pandas
python-scikit-learn
python-scipy
python-umap-learn))
(define-public python-intervaltree
(package
(name "python-intervaltree")
- (version "3.0.2")
+ (version "3.1.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "intervaltree" version))
(sha256
(base32
- "0wz234g6irlm4hivs2qzmnywk0ss06ckagwh15nflkyb3p462kyb"))))
+ "0bcm6c6r4ck9nfj9xwz4rm2swc5lrjvmw3lyl6rgj639jf41nawh"))))
(build-system python-build-system)
(arguments
`(#:phases
(substitute* '("requirements.txt"
"cooler.egg-info/requires.txt")
(("cytoolz.*<.*0.11") "cytoolz"))))
+ ;; This version of flake8 just won't work with this version of
+ ;; pytest, because of dependency pinning.
+ (add-after 'unpack 'do-not-use-flake8
+ (lambda _
+ (substitute* "setup.cfg"
+ (("addopts = --flake8") "addopts = "))))
(add-after 'unpack 'patch-tests
(lambda _
(substitute* "tests/test_create.py"
"access to genome.ucsc.edu\")\n"
"def test_roundtrip")))
(substitute* "tests/test_util.py"
- (("def test_fetch_chromsizes")
- (string-append "@pytest.mark.skip(reason=\"requires network "
- "access to genome.ucsc.edu\")\n"
- "def test_fetch_chromsizes")))
+ (("def test_fetch_chromsizes")
+ (string-append "@pytest.mark.skip(reason=\"requires network "
+ "access to genome.ucsc.edu\")\n"
+ "def test_fetch_chromsizes"))
+ ;; See https://github.com/open2c/cooler/issues/287
+ (("skipif\\(six.PY2, reason=\"Scipy on Py2 is too old\"")
+ "skip(reason=\"Scipy is too new\""))
;; This test depends on ipytree, which contains a lot of minified
;; JavaScript.
(substitute* "tests/test_fileops.py"
matrices.")
(license license:expat)))
+(define-public python-scanorama
+ (package
+ (name "python-scanorama")
+ (version "1.7.2")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "scanorama" version))
+ (sha256
+ (base32
+ "0il7bf4c7vli2dm2jx7dskh3ymgv8nmk0y90jzgfrnqjzh250x5w"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ (list python-annoy
+ python-fbpca
+ python-geosketch
+ python-intervaltree
+ python-matplotlib
+ python-numpy
+ python-scikit-learn
+ python-scipy))
+ (home-page "https://github.com/brianhie/scanorama")
+ (synopsis "Panoramic stitching of heterogeneous single cell transcriptomic data")
+ (description
+ "Scanorama enables batch-correction and integration of heterogeneous
+scRNA-seq datasets, which is described in the paper \"Efficient integration of
+heterogeneous single-cell transcriptomes using Scanorama\" by Brian Hie, Bryan
+Bryson, and Bonnie Berger.")
+ (license license:expat)))
+
(define-public r-pore
(package
(name "r-pore")
sequence for paired-ended data, for which this information is not available.")
(license license:gpl3+)))
-(define-public pplacer
- (let ((commit "807f6f3"))
- (package
- (name "pplacer")
- ;; The commit should be updated with each version change.
- (version "1.1.alpha19")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/matsen/pplacer")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn"))))
- (build-system ocaml-build-system)
- (arguments
- `(#:modules ((guix build ocaml-build-system)
- (guix build utils)
- (ice-9 ftw))
- #:phases
- (modify-phases %standard-phases
- (delete 'configure)
- (add-after 'unpack 'fix-build-with-latest-ocaml
- (lambda _
- (substitute* "myocamlbuild.ml"
- (("dep \\[\"c_pam\"\\]" m)
- (string-append "flag [\"ocaml\"; \"compile\"] (A \"-unsafe-string\");\n"
- m))
- (("let run_and_read" m)
- (string-append "
-let split s ch =
- let x = ref [] in
- let rec go s =
- let pos = String.index s ch in
- x := (String.before s pos)::!x;
- go (String.after s (pos + 1))
- in
- try go s
- with Not_found -> !x
-let split_nl s = split s '\\n'
-let before_space s =
- try String.before s (String.index s ' ')
- with Not_found -> s
-
-" m))
- (("run_and_read \"ocamlfind list \\| cut -d' ' -f1\"" m)
- (string-append "List.map before_space (split_nl & " m ")"))
- ((" blank_sep_strings &") "")
- ((" Lexing.from_string &") ""))
- #t))
- (add-after 'unpack 'replace-bundled-cddlib
- (lambda* (#:key inputs #:allow-other-keys)
- (let* ((cddlib-src (assoc-ref inputs "cddlib-src"))
- (local-dir "cddlib_guix"))
- (mkdir local-dir)
- (with-directory-excursion local-dir
- (invoke "tar" "xvf" cddlib-src))
- (let ((cddlib-src-folder
- (string-append local-dir "/"
- (list-ref (scandir local-dir) 2)
- "/lib-src")))
- (for-each make-file-writable (find-files "cdd_src" ".*"))
- (for-each
- (lambda (file)
- (copy-file file
- (string-append "cdd_src/" (basename file))))
- (find-files cddlib-src-folder ".*[ch]$")))
- #t)))
- (add-after 'unpack 'fix-makefile
- (lambda _
- ;; Remove system calls to 'git'.
- (substitute* "Makefile"
- (("^DESCRIPT:=pplacer-.*")
- (string-append
- "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n")))
- (substitute* "myocamlbuild.ml"
- (("git describe --tags --long .*\\\" with")
- (string-append
- "echo -n v" ,version "-" ,commit "\" with")))
- #t))
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin")))
- (copy-recursively "bin" bin))
- #t)))
- #:ocaml ,ocaml-4.07
- #:findlib ,ocaml4.07-findlib))
- (inputs
- `(("zlib" ,zlib "static")
- ("gsl" ,gsl-static)
- ("ocaml-ounit" ,(package-with-ocaml4.07 ocaml-ounit))
- ("ocaml-batteries" ,(package-with-ocaml4.07 ocaml-batteries))
- ("ocaml-camlzip" ,(package-with-ocaml4.07 camlzip))
- ("ocaml-csv" ,(package-with-ocaml4.07 ocaml-csv))
- ("ocaml-sqlite3" ,(package-with-ocaml4.07 ocaml-sqlite3))
- ("ocaml-xmlm" ,(package-with-ocaml4.07 ocaml-xmlm))
- ("ocaml-mcl" ,(package-with-ocaml4.07 ocaml-mcl))
- ("ocaml-gsl" ,ocaml4.07-gsl-1)
- ("sqlite:static" ,sqlite "static")))
- (native-inputs
- `(("cddlib-src" ,(package-source cddlib))
- ("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild))
- ("pkg-config" ,pkg-config)))
- (propagated-inputs
- (list pplacer-scripts))
- (synopsis "Phylogenetic placement of biological sequences")
- (description
- "Pplacer places query sequences on a fixed reference phylogenetic tree
-to maximize phylogenetic likelihood or posterior probability according to a
-reference alignment. Pplacer is designed to be fast, to give useful
-information about uncertainty, and to offer advanced visualization and
-downstream analysis.")
- (home-page "https://matsen.fhcrc.org/pplacer/")
- (license license:gpl3))))
-
-;; This package is installed alongside 'pplacer'. It is a separate package so
-;; that it can use the python-build-system for the scripts that are
-;; distributed alongside the main OCaml binaries.
-(define pplacer-scripts
- (package
- (inherit pplacer)
- (name "pplacer-scripts")
- (build-system python-build-system)
- (arguments
- `(#:python ,python-2
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'enter-scripts-dir
- (lambda _ (chdir "scripts") #t))
- (replace 'check
- (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))
- (add-after 'install 'wrap-executables
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append out "/bin")))
- (let ((path (string-append
- (assoc-ref inputs "hmmer") "/bin:"
- (assoc-ref inputs "infernal") "/bin")))
- (display path)
- (wrap-program (string-append bin "/refpkg_align.py")
- `("PATH" ":" prefix (,path))))
- (let ((path (string-append
- (assoc-ref inputs "hmmer") "/bin")))
- (wrap-program (string-append bin "/hrefpkg_query.py")
- `("PATH" ":" prefix (,path)))))
- #t)))))
- (inputs
- `(("infernal" ,infernal)
- ("hmmer" ,hmmer)))
- (propagated-inputs
- `(("python-biopython" ,python2-biopython)
- ("taxtastic" ,taxtastic)))
- (synopsis "Pplacer Python scripts")))
-
(define-public checkm
(package
(name "checkm")
files.")
(license license:expat))))
+(define-public python-ctxcore
+ (package
+ (name "python-ctxcore")
+ (version "0.1.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/aertslab/ctxcore")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "16nlj7z8pirgjad7vlgm7226b3hpw4a7n967vyfg26dsf5n8k70d"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'build 'pretend-version
+ ;; The version string is usually derived via setuptools-scm, but
+ ;; it doesn't work without the .git directory.
+ (lambda _
+ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))))))
+ (propagated-inputs
+ (list python-cytoolz
+ python-numba
+ python-frozendict
+ python-numpy
+ python-pandas
+ python-pyyaml
+ python-pyarrow-0.16
+ python-tqdm))
+ (native-inputs
+ (list python-pytest
+ python-setuptools-scm))
+ (home-page "https://github.com/aertslab/ctxcore")
+ (synopsis "Core functions for pycisTarget and the SCENIC tool suite")
+ (description
+ "ctxcore is part of the SCENIC suite of tools. It provides core functions for
+pycisTarget and SCENIC.")
+ (license license:gpl3+)))
+
+(define-public python-arboreto
+ (package
+ (name "python-arboreto")
+ (version "0.1.6")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/aertslab/arboreto")
+ (commit "2f475dca08f47a60acc2beb8dd897e77b7495ca4")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0l0im8ay7l2d24f7vaha454vsaha9s36bfqhbijg3b8ir8apsd7l"))))
+ (build-system python-build-system)
+ ;; Lots of tests fail because python-distributed fails to start the
+ ;; "Nanny" process.
+ (arguments '(#:tests? #false))
+ (propagated-inputs
+ (list python-bokeh
+ python-dask
+ python-distributed
+ python-numpy
+ python-pandas
+ python-scikit-learn
+ python-scipy
+ python-tornado-6))
+ (home-page "https://github.com/aertslab/arboreto")
+ (synopsis "Gene regulatory network inference using tree-based ensemble regressors")
+ (description
+ "This package implements scalable gene regulatory network inference using
+tree-based ensemble regressors.")
+ (license license:bsd-3)))
+
+(define-public pyscenic
+ (package
+ (name "pyscenic")
+ (version "0.11.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/aertslab/pySCENIC")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0pbmmr1zdb1vbbs6wx357s59d13pna6x03wq8blj6ckjws8bbq73"))))
+ (build-system python-build-system)
+ (arguments
+ `(#: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")))
+ (replace 'check
+ (lambda _
+ (invoke "pytest" "-v"))))))
+ (propagated-inputs
+ (list python-ctxcore
+ python-cytoolz
+ python-multiprocessing-on-dill
+ python-llvmlite
+ python-numba
+ python-attrs
+ python-frozendict
+ python-numpy
+ python-pandas
+ python-cloudpickle
+ python-dask
+ python-distributed
+ python-arboreto
+ python-boltons
+ python-setuptools
+ python-pyyaml
+ python-tqdm
+ python-interlap
+ python-umap-learn
+ python-loompy
+ python-networkx
+ python-scipy
+ python-fsspec
+ python-requests
+ python-aiohttp
+ python-scikit-learn))
+ (native-inputs
+ (list python-pytest))
+ (home-page "https://scenic.aertslab.org/")
+ (synopsis "Single-Cell regulatory network inference and clustering")
+ (description
+ "pySCENIC is a Python implementation of the SCENIC pipeline (Single-Cell
+rEgulatory Network Inference and Clustering) which enables biologists to infer
+transcription factors, gene regulatory networks and cell types from
+single-cell RNA-seq data.")
+ (license license:gpl3+)))
+
+(define-public python-ikarus
+ (package
+ (name "python-ikarus")
+ (version "0.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "ikarus" version))
+ (sha256
+ (base32
+ "086czpvj4yafz4vrq5rx2gy0bj2l8nzwnkk0gw8qvy4w133xjysy"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #false
+ #:phases
+ (modify-phases %standard-phases
+ ;; See https://github.com/BIMSBbioinfo/ikarus/issues/12
+ (add-after 'unpack 'fix-issue-12
+ (lambda _
+ (substitute* "ikarus/classifier.py"
+ (("pyscenic.genesig") "ctxcore.genesig"))))
+ ;; Numba needs a writable dir to cache functions.
+ (add-before 'check 'set-numba-cache-dir
+ (lambda _
+ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
+ (propagated-inputs
+ (list python-numpy
+ python-pandas
+ python-scipy
+ python-scanpy
+ python-anndata
+ python-ctxcore ;because of issue 12
+ pyscenic))
+ (home-page "https://github.com/BIMSBbioinfo/ikarus")
+ (synopsis "Machine learning classifier of tumor cells")
+ (description
+ "ikarus is a stepwise machine learning pipeline that tries to cope with a task
+of distinguishing tumor cells from normal cells. Leveraging multiple
+annotated single cell datasets it can be used to define a gene set specific to
+tumor cells. First, the latter gene set is used to rank cells and then to
+train a logistic classifier for the robust classification of tumor and normal
+cells. Finally, sensitivity is increased by propagating the cell labels based
+on a custom cell-cell network. ikarus is tested on multiple single cell
+datasets to ascertain that it achieves high sensitivity and specificity in
+multiple experimental contexts.")
+ (license license:expat)))
+
(define-public vbz-compression
(package
(name "vbz-compression")
;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9.
(license (list license:gpl2 license:expat)))))
+(define-public sylamer
+ (package
+ (name "sylamer")
+ (version "18-131")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/micans/sylamer/")
+ (commit "aa75c3584797c0c15f860addb645f7bc1dd7627d")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1ddiwlrdghhb4574rvfw0brjp9gs5l6nfsy82h0m4mvz1dr3gkj5"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:tests? #f ; no test target
+ #:make-flags
+ #~(list (string-append "GSLPREFIX=" #$(this-package-input "gsl")))
+ #:phases
+ '(modify-phases %standard-phases
+ (replace 'configure
+ (lambda* (#:key outputs #:allow-other-keys)
+ (substitute* "Makefile"
+ (("cp sylamer \\$\\(HOME\\)/local/bin")
+ (string-append "install -D -t " (assoc-ref outputs "out")
+ "/bin sylamer")))
+ (install-file "Makefile" "src")
+ (chdir "src"))))))
+ (inputs (list gsl zlib))
+ (home-page "https://www.ebi.ac.uk/research/enright/software/sylamer")
+ (synopsis "Asses microRNA binding and siRNA off-target effects")
+ (description "Sylamer is a system for finding significantly over or
+under-represented words in sequences according to a sorted gene list.
+Typically it is used to find significant enrichment or depletion of microRNA
+or siRNA seed sequences from microarray expression data. Sylamer is extremely
+fast and can be applied to genome-wide datasets with ease. Results are
+plotted in terms of a significance landscape plot. These plots show
+significance profiles for each word studied across the sorted genelist.")
+ (license license:gpl3+)))
+
(define-public multichoose
(package
(name "multichoose")
(propagated-inputs
(list libxml2))
(native-inputs
- (list check-0.14 swig))
+ (list check swig))
(home-page "http://sbml.org/Software/libSBML")
(synopsis "Process SBML files and data streams")
(description "LibSBML is a library to help you read, write, manipulate,
(define-public kraken2
(package
(name "kraken2")
- (version "2.1.1")
+ (version "2.1.2")
(source (origin
(method git-fetch)
(uri (git-reference
(file-name (git-file-name name version))
(sha256
(base32
- "0h7a7vygd7y5isbrnc6srwq6xj1rmyd33pm8mmcgfkmlxlg5vkg3"))))
+ "1pl6ml1ldg2hnhy8ps56q0fl1wq3g91qkhinj6pb4yjjhv1rxsjf"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #false ; there are none
(base32
"1023hadgcsgi53kz53ql45207hfizf9sw57z0qij3ay1bx68zbpm"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #false)) ;no tests
(native-inputs
(list python-cython python-nose2))
;; The package mainly consists of a command-line tool, but also has a
(license license:mpl2.0)))
(define-public python-pyvcf
- (package
- (name "python-pyvcf")
- (version "0.6.8")
- ;; Use git, because the PyPI tarballs lack test data.
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
+ (let ((commit "476169cd457ba0caa6b998b301a4d91e975251d9")
+ (revision "0"))
+ (package
+ (name "python-pyvcf")
+ (version (git-version "0.6.8" revision commit))
+ ;; Use git, because the PyPI tarballs lack test data.
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
(url "https://github.com/jamescasbon/PyVCF.git")
;; Latest release is not tagged.
- (commit "bfcedb9bad1a14074ac4526ffdb610611e073810")))
- (file-name (git-file-name name version))
- (sha256
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
(base32
- "0c7lsssns3zp8fh2ibllzzra003srg9vbxqzmq6654akbzdb7lrf"))))
- (build-system python-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'patch-sample-script
- (lambda _
- ;; Add Python 3 compatibility to this sample script.
- (substitute* "scripts/vcf_sample_filter.py"
- (("print (.*)\n" _ arg)
- (string-append "print(" arg ")\n")))))
- (add-after 'install 'remove-installed-tests
- ;; Do not install test files.
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (delete-file-recursively (string-append
+ "0qf9lwj7r2hjjp4bd4vc7nayrhblfm4qcqs4dbd43a6p4bj2jv5p"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-sample-script
+ (lambda _
+ ;; Add Python 3 compatibility to this sample script.
+ (substitute* "scripts/vcf_sample_filter.py"
+ (("print (.*)\n" _ arg)
+ (string-append "print(" arg ")\n")))))
+ (add-after 'install 'remove-installed-tests
+ ;; Do not install test files.
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (delete-file-recursively (string-append
(site-packages inputs outputs)
"/vcf/test")))))))
- (native-inputs
- ;; Older setuptools is needed for use_2to3.
- (list python-cython python-setuptools))
- (propagated-inputs
- (list python-pysam python-rpy2))
- (home-page "https://github.com/jamescasbon/PyVCF")
- (synopsis "Variant Call Format parser for Python")
- (description "This package provides a @acronym{VCF,Variant Call Format}
+ (native-inputs
+ ;; Older setuptools is needed for use_2to3.
+ (list python-cython python-setuptools-for-tensorflow))
+ (propagated-inputs
+ (list python-pysam python-rpy2))
+ (home-page "https://github.com/jamescasbon/PyVCF")
+ (synopsis "Variant Call Format parser for Python")
+ (description "This package provides a @acronym{VCF,Variant Call Format}
parser for Python.")
- (license license:expat)))
+ (license license:expat))))
(define-public nanosv
(package
both types of files.")
(license license:expat)))
+(define-public mudskipper
+ (package
+ (name "mudskipper")
+ (version "0.1.0")
+ (source (origin
+ (method url-fetch)
+ (uri (crate-uri "mudskipper" version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1y7fnlz6irmxdmv6bxzm95w4ws4vzldlrh8npvgxmdnrz9pgb1dv"))))
+ (build-system cargo-build-system)
+ (arguments
+ `(#:tests? #false ;fail because the "mudskipper" crate cannot be found
+ #:cargo-inputs
+ (("rust-bio" ,rust-bio-0.39)
+ ("rust-bio-types" ,rust-bio-types-0.12)
+ ("rust-clap" ,rust-clap-2)
+ ("rust-coitrees" ,rust-coitrees-0.2)
+ ("rust-env-logger" ,rust-env-logger-0.9)
+ ("rust-fnv" ,rust-fnv-1)
+ ("rust-indicatif" ,rust-indicatif-0.16)
+ ("rust-libradicl" ,rust-libradicl-0.4)
+ ("rust-linecount" ,rust-linecount-0.1)
+ ("rust-log" ,rust-log-0.4)
+ ("rust-num-cpus" ,rust-num-cpus-1)
+ ("rust-rust-htslib" ,rust-rust-htslib-0.38))))
+ (native-inputs
+ (list cmake pkg-config))
+ (inputs
+ (list zlib xz))
+ (home-page "https://github.com/OceanGenomics/mudskipper")
+ (synopsis "Convert genomic alignments to transcriptomic BAM/RAD files.")
+ (description "Mudskipper is a tool for projecting genomic alignments to
+transcriptomic coordinates.")
+ (license license:bsd-3)))
+
(define-public r-ascat
(package
(name "r-ascat")
cytometry and imaging data.")
(license license:expat))))
+(define-public r-compgenomrdata
+ (let ((commit "24484cb77631e1123ead6c329b9d62c160e600c6")
+ (revision "1"))
+ (package
+ (name "r-compgenomrdata")
+ (version (git-version "0.1.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/compgenomr/compGenomRData")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "06gdvz4m4qlb1ylv10qfx09zv4c95cm7nps4y2s67m946kv8czv8"))))
+ (properties `((upstream-name . "compGenomRData")))
+ (build-system r-build-system)
+ (home-page "https://github.com/compgenomr/compGenomRData")
+ (synopsis "Data for Computational Genomics with R book")
+ (description "This package provides data for the book \"Computational
+Genomics with R\".")
+ (license license:gpl3))))
+
(define-public r-cytonorm
(let ((commit "e4b9d343ee65db3c422800f1db3e77c25abde987")
(revision "1"))
interest.")
(license license:gpl2+))))
+(define-public r-kbet
+ (let ((commit "f35171dfb04c7951b8a09ac778faf7424c4b6bc0")
+ (revision "1"))
+ (package
+ (name "r-kbet")
+ (version (git-version "0.99.6" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/theislab/kBET")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1r91prl2kki3zk694vhlmxdlqh0ixlhs8jfcqw6wc7cdsa0nv67k"))))
+ (properties `((upstream-name . "kBET")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-cluster r-fnn r-ggplot2 r-mass r-rcolorbrewer))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/theislab/kBET")
+ (synopsis "k-nearest neighbour batch effect test")
+ (description
+ "This tool detects batch effects in high-dimensional data based on chi^2-test.")
+ ;; Any version of the GPL
+ (license license:gpl3+))))
+
(define-public ccwl
(package
(name "ccwl")
language.")
(license license:gpl3+)))
+(define-public hh-suite
+ (package
+ (name "hh-suite")
+ (version "3.3.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/soedinglab/hh-suite")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1bcmzg0ii6nkda2xm5jdddbwkgsag7k38j20af0c9chr2mbxwx4d"))
+ (modules '((guix build utils)))
+ (snippet
+ '(delete-file-recursively "lib/simde"))))
+ (build-system cmake-build-system)
+ (arguments '(#:tests? #false)) ;no test target
+ (inputs
+ (list openmpi simde))
+ (native-inputs
+ (list perl pkg-config xxd))
+ (home-page "https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3019-7")
+ (synopsis "Remote protein homology detection suite")
+ (description "The HH-suite is a software package for sensitive protein sequence searching
+based on the pairwise alignment of hidden Markov models (HMMs).")
+ (license license:gpl3+)))
+
(define-public wfmash
(package
(name "wfmash")
module capable of computing base-level alignments for very large sequences.")
(home-page "https://github.com/ekg/wfmash")
(license license:expat)))
+
+(define-public flair
+ (package
+ (name "flair")
+ (version "1.6.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BrooksLabUCSC/flair")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "106swb2q7l20ki58fca1hg95q5f79bgp9gjb0clr2243ycrzyxf8"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:tests? #false ;there are none
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; TODO: implement as a feature of python-build-system (PEP-621,
+ ;; PEP-631, PEP-660)
+ (replace 'build
+ (lambda _
+ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)
+ ;; ZIP does not support timestamps before 1980.
+ (setenv "SOURCE_DATE_EPOCH" "315532800")
+ (invoke "python" "-m" "build" "--wheel" "--no-isolation" ".")))
+ (replace 'install
+ (lambda _
+ (apply invoke "pip" "--no-cache-dir" "--no-input"
+ "install" "--no-deps" "--prefix" #$output
+ (find-files "dist" "\\.whl$")))))))
+ (propagated-inputs
+ (list python-mappy
+ python-ncls
+ python-pybedtools
+ python-pysam
+ python-tqdm))
+ (native-inputs
+ (list python-pypa-build python-setuptools))
+ (home-page "https://flair.readthedocs.io/en/latest/")
+ (synopsis "Full-length alternative isoform analysis of RNA")
+ (description "This package implements FLAIR (Full-Length Alternative
+Isoform analysis of RNA) for the correction, isoform definition, and
+alternative splicing analysis of noisy reads. FLAIR has primarily been used
+for nanopore cDNA, native RNA, and PacBio sequencing reads.")
+ (license license:bsd-3)))
+
+(define-public go-github-com-biogo-graph
+ (package
+ (name "go-github-com-biogo-graph")
+ (version "0.0.0-20150317020928-057c1989faed")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/biogo/graph")
+ (commit (go-version->git-ref version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1kpzs5dfd5dsk4mg1g2qjz1prqd84ixhrcxxnf90hq25vxcnk7lh"))))
+ (build-system go-build-system)
+ (arguments
+ '(#:import-path "github.com/biogo/graph"
+ #:tests? #false)) ;TODO: one of 13 tests fails for unknown reasons
+ (propagated-inputs
+ (list go-gopkg-in-check-v1))
+ (home-page "https://github.com/biogo/graph")
+ (synopsis "Undirected graph analysis for biogo")
+ (description "The package @code{graph} implements graph manipulation
+functions.")
+ (license license:bsd-3)))
+
+(define-public go-github-com-biogo-store-interval
+ (package
+ (name "go-github-com-biogo-store-interval")
+ (version "0.0.0-20201120204734-aad293a2328f")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/biogo/store")
+ (commit (go-version->git-ref version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0skizrp1j6vgbl0g1kmh73picagqlvwckaqs0gkl6rai5lckxj8a"))))
+ (build-system go-build-system)
+ (arguments
+ '(#:import-path "github.com/biogo/store/interval"
+ #:unpack-path "github.com/biogo/store"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1
+ go-github-com-kr-pretty))
+ (home-page "https://github.com/biogo/store")
+ (synopsis "Interval store type for biogo")
+ (description
+ "The @code{store} package provides a number of data store types that are
+useful for bioinformatic analysis.")
+ (license license:bsd-3)))
+
+(define-public go-github-com-biogo-store-kdtree
+ (package
+ (inherit go-github-com-biogo-store-interval)
+ (name "go-github-com-biogo-store-kdtree")
+ (arguments
+ '(#:import-path "github.com/biogo/store/kdtree"
+ #:unpack-path "github.com/biogo/store"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1
+ go-github-com-kr-pretty))
+ (synopsis "kdtree store type for biogo")))
+
+(define-public go-github-com-biogo-store-llrb
+ (package
+ (inherit go-github-com-biogo-store-interval)
+ (name "go-github-com-biogo-store-llrb")
+ (arguments
+ '(#:import-path "github.com/biogo/store/llrb"
+ #:unpack-path "github.com/biogo/store"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1
+ go-github-com-kr-pretty))
+ (synopsis "LLRB store for biogo")))
+
+(define-public go-github-com-biogo-store-step
+ (package
+ (inherit go-github-com-biogo-store-interval)
+ (name "go-github-com-biogo-store-step")
+ (arguments
+ '(#:import-path "github.com/biogo/store/step"
+ #:unpack-path "github.com/biogo/store"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1
+ go-github-com-kr-pretty))
+ (synopsis "Step store for biogo")))
+
+(define-public go-github-com-biogo-hts-bam
+ (package
+ (name "go-github-com-biogo-hts-bam")
+ (version "1.4.3")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/biogo/hts")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "013ga6ilc4m3hyfr3yyiva9g4vs81afhj73v2sy7r75b5zxw7lx1"))))
+ (build-system go-build-system)
+ (arguments
+ '(#:import-path "github.com/biogo/hts/bam"
+ #:unpack-path "github.com/biogo/hts"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1))
+ (home-page "https://github.com/biogo/hts")
+ (synopsis "HTS BAM module for biogo")
+ (description "This package provides tools for handling BAM files.")
+ (license license:bsd-3)))
+
+(define-public go-github-com-biogo-hts-sam
+ (package
+ (inherit go-github-com-biogo-hts-bam)
+ (name "go-github-com-biogo-hts-sam")
+ (arguments
+ '(#:import-path "github.com/biogo/hts/sam"
+ #:unpack-path "github.com/biogo/hts"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1))
+ (synopsis "HTS SAM module for biogo")
+ (description "This package provides tools for handling SAM files.")))
+
+(define-public go-github-com-biogo-hts-tabix
+ (package
+ (inherit go-github-com-biogo-hts-bam)
+ (name "go-github-com-biogo-hts-tabix")
+ (arguments
+ '(#:import-path "github.com/biogo/hts/tabix"
+ #:unpack-path "github.com/biogo/hts"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1))
+ (synopsis "HTS Tabix module for biogo")
+ (description "This package provides tools for handling Tabix files.")))
+
+(define-public go-github-com-biogo-hts-bgzf
+ (package
+ (inherit go-github-com-biogo-hts-bam)
+ (name "go-github-com-biogo-hts-bgzf")
+ (arguments
+ '(#:import-path "github.com/biogo/hts/bgzf"
+ #:unpack-path "github.com/biogo/hts"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1))
+ (synopsis "HTS bgzf module for biogo")
+ (description "This package provides tools for handling bgzf files.")))
+
+(define-public go-github-com-biogo-hts-cram
+ (package
+ (inherit go-github-com-biogo-hts-bam)
+ (name "go-github-com-biogo-hts-cram")
+ (arguments
+ '(#:import-path "github.com/biogo/hts/cram"
+ #:unpack-path "github.com/biogo/hts"
+ #:tests? #false)) ;require network access
+ (propagated-inputs
+ (list go-gopkg-in-check-v1
+ go-github.com-ulikunitz-xz
+ go-github-com-kortschak-utter))
+ (synopsis "HTS CRAM module for biogo")
+ (description "This package provides tools for handling CRAM files.")))
+
+(define-public go-github-com-biogo-hts-csi
+ (package
+ (inherit go-github-com-biogo-hts-bam)
+ (name "go-github-com-biogo-hts-csi")
+ (arguments
+ '(#:import-path "github.com/biogo/hts/csi"
+ #:unpack-path "github.com/biogo/hts"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1))
+ (synopsis "Coordinate sorted indexing for biogo")
+ (description "This package implements CSIv1 and CSIv2 coordinate sorted
+indexing.")))
+
+(define-public go-github-com-biogo-hts-fai
+ (package
+ (inherit go-github-com-biogo-hts-bam)
+ (name "go-github-com-biogo-hts-fai")
+ (arguments
+ '(#:import-path "github.com/biogo/hts/fai"
+ #:unpack-path "github.com/biogo/hts"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1))
+ (synopsis "Fasta sequence file index handling for biogo")
+ (description "This package implements FAI fasta sequence file index
+handling.")))
+
+(define-public go-github-com-biogo-biogo
+ (package
+ (name "go-github-com-biogo-biogo")
+ (version "1.0.4")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/biogo/biogo")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0ali1mqf3dc26myv6l7wmqfr8i25461rbq3qdad8s0wi29622199"))))
+ (build-system go-build-system)
+ (arguments
+ '(#:import-path "github.com/biogo/biogo"))
+ (propagated-inputs
+ (list go-gopkg-in-check-v1
+ go-github-com-biogo-store-interval
+ go-github-com-biogo-store-kdtree
+ go-github-com-biogo-store-llrb
+ go-github-com-biogo-store-step
+ go-github-com-biogo-hts-bam
+ go-github-com-biogo-graph))
+ (home-page "https://github.com/biogo/biogo")
+ (synopsis "Bioinformatics library for Go")
+ (description
+ "Bíogo is a bioinformatics library for the Go language.")
+ (license license:bsd-3)))
+
+;;;
+;;; Avoid adding new packages to the end of this file. To reduce the chances
+;;; of a merge conflict, place them above by existing packages with similar
+;;; functionality or similar names.
+;;;
HCoop / jackhill / guix / guix.git / blobdiff