;; 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
(inputs
(list gsl openblas zlib))
(native-inputs
- `(("catch" ,catch-framework2-1)
+ `(("catch" ,catch2-1)
("perl" ,perl)
("shunit2" ,shunit2)
("which" ,which)))
(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"))
;; (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")
(define-public pigx-bsseq
(package
(name "pigx-bsseq")
- (version "0.1.7")
+ (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
- "1hfiignq3410dbl6f67vc6zr69abknpcgxixx475dspky2jb5lyn"))))
+ "1s8zgrqxabrawrgkga5rmgb0gyzj7ck47p3rkicjkfv7r2yjy0d7"))))
(build-system gnu-build-system)
(arguments
`(;; TODO: tests currently require 12+GB of RAM. See
(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))
(license license:gpl3+)))
(define-public r-dyngen
- (let ((commit "37fd1798fcbd41093fb3d7775bb2d268e2fc82b6")
- (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")))
- (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
+ (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))))
+ (license license:expat)))
;; Needed for r-liana
(define-public r-omnipathr/devel
(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"
(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")
(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")
(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