;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
+;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (guix build-system ant)
#:use-module (guix build-system gnu)
#:use-module (guix build-system cmake)
+ #:use-module (guix build-system go)
#:use-module (guix build-system haskell)
#:use-module (guix build-system meson)
#:use-module (guix build-system ocaml)
#:use-module (gnu packages documentation)
#:use-module (gnu packages databases)
#:use-module (gnu packages datastructures)
+ #:use-module (gnu packages dlang)
#:use-module (gnu packages file)
#:use-module (gnu packages flex)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gd)
- #:use-module (gnu packages gtk)
+ #:use-module (gnu packages golang)
#:use-module (gnu packages glib)
#:use-module (gnu packages graph)
#:use-module (gnu packages groff)
+ #:use-module (gnu packages gtk)
#:use-module (gnu packages guile)
#:use-module (gnu packages guile-xyz)
#:use-module (gnu packages haskell-check)
#:use-module (gnu packages java)
#:use-module (gnu packages java-compression)
#:use-module (gnu packages jemalloc)
- #:use-module (gnu packages dlang)
#:use-module (gnu packages linux)
#:use-module (gnu packages lisp-xyz)
#:use-module (gnu packages logging)
(define-public bedtools
(package
(name "bedtools")
- (version "2.27.1")
+ (version "2.29.2")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/arq5x/bedtools2/releases/"
"bedtools-" version ".tar.gz"))
(sha256
(base32
- "1ndg5yknrxl4djx8ddzgk12rrbiidfpmkkg5z3f95jzryfxarhn8"))))
+ "0m3hk6548846w83a9s5drsczvy67n2azx41kj71n03klb2gbzwg3"))))
(build-system gnu-build-system)
(arguments
'(#:test-target "test"
#:phases
(modify-phases %standard-phases
(delete 'configure))))
- (native-inputs `(("python" ,python-2)))
+ (native-inputs
+ `(("python" ,python-wrapper)))
(inputs
`(("samtools" ,samtools)
("zlib" ,zlib)))
allows one to intersect, merge, count, complement, and shuffle genomic
intervals from multiple files in widely-used genomic file formats such as BAM,
BED, GFF/GTF, VCF.")
- (license license:gpl2)))
+ (license license:expat)))
;; Later releases of bedtools produce files with more columns than
;; what Ribotaper expects.
(define-public python-pybedtools
(package
(name "python-pybedtools")
- (version "0.8.0")
+ (version "0.8.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "pybedtools" version))
(sha256
(base32
- "1xl454ijvd4dzfvqgfahad49b49j7qy710fq9xh1rvk42z6x5ssf"))))
+ "14w5i40gi25clrr7h4wa2pcpnyipya8hrqi7nq77553zc5wf0df0"))))
(build-system python-build-system)
(arguments
`(#:modules ((ice-9 ftw)
;; (see: https://github.com/daler/pybedtools/issues/192).
(("def test_getting_example_beds")
"def _do_not_test_getting_example_beds"))
+ ;; This issue still occurs on python2
+ (substitute* "pybedtools/test/test_issues.py"
+ (("def test_issue_303")
+ "def _test_issue_303"))
#t))
;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM.
;; build system.
(license license:gpl2+)))
(define-public python2-pybedtools
- (package-with-python2 python-pybedtools))
+ (let ((pybedtools (package-with-python2 python-pybedtools)))
+ (package
+ (inherit pybedtools)
+ (native-inputs
+ `(("python2-pathlib" ,python2-pathlib)
+ ,@(package-native-inputs pybedtools))))))
(define-public python-biom-format
(package
(define-public crossmap
(package
(name "crossmap")
- (version "0.2.9")
+ (version "0.3.8")
(source (origin
(method url-fetch)
(uri (pypi-uri "CrossMap" version))
(sha256
(base32
- "1byhclrqnqpvc1rqkfh4jwj6yhn0x9y7jk47i0qcjlhk0pjkw92p"))))
+ "1sb2f2qbxya4fzw3yjl09vbrs8vfmw22zrygrvz004sf9gb1vkan"))))
(build-system python-build-system)
- (arguments `(#:python ,python-2))
(inputs
- `(("python-bx-python" ,python2-bx-python)
- ("python-numpy" ,python2-numpy)
- ("python-pysam" ,python2-pysam)
+ `(("python-bx-python" ,python-bx-python)
+ ("python-numpy" ,python-numpy)
+ ("python-pybigwig" ,python-pybigwig)
+ ("python-pysam" ,python-pysam)
("zlib" ,zlib)))
(native-inputs
- `(("python-cython" ,python2-cython)
- ("python-nose" ,python2-nose)))
+ `(("python-cython" ,python-cython)
+ ("python-nose" ,python-nose)))
(home-page "http://crossmap.sourceforge.net/")
(synopsis "Convert genome coordinates between assemblies")
(description
(define-public diamond
(package
(name "diamond")
- (version "0.9.22")
+ (version "0.9.30")
(source (origin
(method git-fetch)
(uri (git-reference
(file-name (git-file-name name version))
(sha256
(base32
- "0bky78v79g3wmdpsd706cscckgw1v09fg8vdd0z8z0d5b97aj9zl"))))
+ "0k6f3kb6cniw11xw6763kkbs1sl0yack7xsy7q5fl5v170ssphq4"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no "check" target
(define-public edirect
(package
(name "edirect")
- (version "12.1.20190829")
+ (version "13.3.20200128")
(source (origin
(method url-fetch)
(uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect"
"/edirect-" version ".tar.gz"))
(sha256
(base32
- "1xb330z28dgp7slrvp8r7rgncsasv9lpcpqim571yg728dq7xdik"))))
+ "093zp7klv81ph0y8mm8d78a9hnpfxbv2kdym70gzdf3vz176rw33"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin (delete-file "Mozilla-CA.tar.gz")
+ (substitute* "rchive.go"
+ ;; This go library does not have any license.
+ (("github.com/fiam/gounidecode/unidecode")
+ "golang.org/rainycape/unidecode"))
+ #t))))
(build-system perl-build-system)
(arguments
`(#:phases
(delete 'configure)
(delete 'build)
(delete 'check) ; simple check after install
+ (add-after 'unpack 'patch-programs
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; Ignore errors about missing xtract.Linux and rchive.Linux.
+ (substitute* "pm-refresh"
+ (("cat \\\"\\$target")
+ "grep ^[[:digit:]] \"$target"))
+ #t))
(replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (install-file "edirect.pl"
- (string-append (assoc-ref outputs "out") "/bin"))
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
+ (edirect-go (assoc-ref inputs "edirect-go-programs")))
+ (for-each
+ (lambda (file)
+ (install-file file bin))
+ '("archive-pubmed" "asp-cp" "asp-ls" "download-ncbi-data"
+ "download-pubmed" "edirect.pl" "efetch" "epost" "esearch"
+ "fetch-pubmed" "ftp-cp" "ftp-ls" "has-asp" "index-pubmed"
+ "pm-prepare" "pm-refresh" "pm-stash" "pm-collect"
+ "pm-index" "pm-invert" "pm-merge" "pm-promote"))
+ (symlink (string-append edirect-go "/bin/xtract.Linux")
+ (string-append bin "/xtract"))
+ (symlink (string-append edirect-go "/bin/rchive.Linux")
+ (string-append bin "/rchive")))
#t))
(add-after 'install 'wrap-program
(lambda* (#:key outputs #:allow-other-keys)
- ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
- (let* ((out (assoc-ref outputs "out"))
+ ;; Make sure everything can run in a pure environment.
+ (let ((out (assoc-ref outputs "out"))
(path (getenv "PERL5LIB")))
- (wrap-program (string-append out "/bin/edirect.pl")
- `("PERL5LIB" ":" prefix (,path))))
- #t))
+ (for-each
+ (lambda (file)
+ (wrap-program file
+ `("PERL5LIB" ":" prefix (,path)))
+ (wrap-program file
+ `("PATH" ":" prefix (,(string-append out "/bin")
+ ,(dirname (which "sed"))
+ ,(dirname (which "gzip"))
+ ,(dirname (which "grep"))
+ ,(dirname (which "perl"))
+ ,(dirname (which "uname"))))))
+ (find-files out ".")))
+ #t))
(add-after 'wrap-program 'check
(lambda* (#:key outputs #:allow-other-keys)
(invoke (string-append (assoc-ref outputs "out")
"-filter" "-help")
#t)))))
(inputs
- `(("perl-html-parser" ,perl-html-parser)
+ `(("edirect-go-programs" ,edirect-go-programs)
+ ("perl-html-parser" ,perl-html-parser)
("perl-encode-locale" ,perl-encode-locale)
("perl-file-listing" ,perl-file-listing)
("perl-html-tagset" ,perl-html-tagset)
extraction of data from document summaries or other results that are returned
in structured XML format. This can eliminate the need for writing custom
software to answer ad hoc questions.")
+ (native-search-paths
+ ;; Ideally this should be set for LWP somewhere.
+ (list (search-path-specification
+ (variable "PERL_LWP_SSL_CA_FILE")
+ (file-type 'regular)
+ (separator #f)
+ (files '("/etc/ssl/certs/ca-certificates.crt")))))
(license license:public-domain)))
+(define-public edirect-go-programs
+ (package
+ (inherit edirect)
+ (name "edirect-go-programs")
+ (build-system go-build-system)
+ (arguments
+ `(#:install-source? #f
+ #:tests? #f ; No tests.
+ #:import-path "ncbi.nlm.nih.gov/entrez/edirect"
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'build
+ (lambda* (#:key import-path #:allow-other-keys)
+ (with-directory-excursion (string-append "src/" import-path)
+ (invoke "go" "build" "-v" "-x" "j2x.go")
+ (invoke "go" "build" "-v" "-x" "t2x.go")
+ (invoke "go" "build" "-v" "-x" "-o"
+ "xtract.Linux" "xtract.go" "common.go")
+ (invoke "go" "build" "-v" "-x" "-o"
+ "rchive.Linux" "rchive.go" "common.go")
+ (invoke "go" "build" "-v" "-x" "-o" "symbols.Linux" "s2p.go"))))
+ (replace 'install
+ (lambda* (#:key outputs import-path #:allow-other-keys)
+ (let ((dest (string-append (assoc-ref outputs "out") "/bin"))
+ (source (string-append "src/" import-path "/")))
+ (for-each (lambda (file)
+ (format #t "installing ~a~%" file)
+ (install-file (string-append source file) dest))
+ '("j2x" "t2x" "symbols.Linux" "xtract.Linux" "rchive.Linux"))
+ #t))))))
+ (native-inputs '())
+ (propagated-inputs '())
+ (inputs
+ `(("go-github-com-fatih-color" ,go-github-com-fatih-color)
+ ("go-github-com-fogleman-gg" ,go-github-com-fogleman-gg)
+ ("go-github-com-gedex-inflector" ,go-github-com-gedex-inflector)
+ ("go-github-com-golang-freetype" ,go-github-com-golang-freetype)
+ ("go-github-com-klauspost-cpuid" ,go-github-com-klauspost-cpuid)
+ ("go-github-com-pbnjay-memory" ,go-github-com-pbnjay-memory)
+ ("go-github-com-surgebase-porter2" ,go-github-com-surgebase-porter2)
+ ("go-golang-org-rainycape-unidecode" ,go-golang-org-rainycape-unidecode)
+ ("go-golang-org-x-image" ,go-golang-org-x-image)
+ ("go-golang-org-x-text" ,go-golang-org-x-text)))))
+
(define-public exonerate
(package
(name "exonerate")
(define-public macs
(package
(name "macs")
- (version "2.1.1.20160309")
+ (version "2.2.6")
(source (origin
- (method url-fetch)
- (uri (pypi-uri "MACS2" version))
+ ;; The PyPi tarball does not contain tests.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/taoliu/MACS.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "09ixspd1vcqmz1c81ih70xs4m7qml2iy5vyx1y74zww3iy1vl210"))))
+ "1c5gxr0mk6hkd4vclf0k00wvyvzw2vrmk52c85338p7aqjwg6n15"))))
(build-system python-build-system)
(arguments
- `(#:python ,python-2 ; only compatible with Python 2.7
- #:tests? #f)) ; no test target
+ `(#:phases
+ (modify-phases %standard-phases
+ (delete 'check)
+ (add-after 'install 'check
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (add-installed-pythonpath inputs outputs)
+ (invoke "pytest" "-v"))))))
(inputs
- `(("python-numpy" ,python2-numpy)))
+ `(("python-numpy" ,python-numpy)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
(home-page "https://github.com/taoliu/MACS/")
(synopsis "Model based analysis for ChIP-Seq data")
(description
(define-public proteinortho
(package
(name "proteinortho")
- (version "5.16b")
- (source
- (origin
- (method url-fetch)
- (uri
- (string-append
- "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v"
- version "_src.tar.gz"))
- (sha256
- (base32
- "1wl0dawpssqwfjvr651r4wlww8hhjin8nba6xh71ks7sbypx886j"))))
+ (version "6.0.14")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.com/paulklemm_PHD/proteinortho.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0pmy617zy2z2w6hjqxjhf3rzikf5n3mpia80ysq8233vfr7wrzff"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; remove pre-built scripts
+ (delete-file-recursively "src/BUILD/")
+ #t))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
+ #:make-flags '("CC=gcc")
#:phases
(modify-phases %standard-phases
(replace 'configure
#t))
(add-after 'install 'wrap-programs
(lambda* (#:key inputs outputs #:allow-other-keys)
- (let* ((path (getenv "PATH"))
- (out (assoc-ref outputs "out"))
- (binary (string-append out "/bin/proteinortho5.pl")))
- (wrap-program binary `("PATH" ":" prefix (,path))))
+ (let ((path (getenv "PATH"))
+ (out (assoc-ref outputs "out")))
+ (for-each (lambda (script)
+ (wrap-script script `("PATH" ":" prefix (,path))))
+ (cons (string-append out "/bin/proteinortho")
+ (find-files out "\\.(pl|py)$"))))
#t)))))
(inputs
- `(("perl" ,perl)
- ("python" ,python-2)
- ("blast+" ,blast+)))
+ `(("guile" ,guile-3.0) ; for wrap-script
+ ("diamond" ,diamond)
+ ("perl" ,perl)
+ ("python" ,python-wrapper)
+ ("blast+" ,blast+)
+ ("lapack" ,lapack)
+ ("openblas" ,openblas)))
+ (native-inputs
+ `(("which" ,which)))
(home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho")
(synopsis "Detect orthologous genes across species")
(description
species. For doing so, it compares similarities of given gene sequences and
clusters them to find significant groups. The algorithm was designed to handle
large-scale data and can be applied to hundreds of species at once.")
- (license license:gpl2+)))
+ (license license:gpl3+)))
(define-public pyicoteo
(package
(define-public rseqc
(package
(name "rseqc")
- (version "2.6.1")
+ (version "3.0.1")
(source
(origin
(method url-fetch)
(string-append "mirror://sourceforge/rseqc/"
"RSeQC-" version ".tar.gz"))
(sha256
- (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- ;; remove bundled copy of pysam
- (delete-file-recursively "lib/pysam")
- (substitute* "setup.py"
- ;; remove dependency on outdated "distribute" module
- (("^from distribute_setup import use_setuptools") "")
- (("^use_setuptools\\(\\)") "")
- ;; do not use bundled copy of pysam
- (("^have_pysam = False") "have_pysam = True"))
- #t))))
+ (base32
+ "0gbb9iyb7swiv5455fm5rg98r7l6qn27v564yllqjd574hncpx6m"))))
(build-system python-build-system)
- (arguments `(#:python ,python-2))
(inputs
- `(("python-cython" ,python2-cython)
- ("python-pysam" ,python2-pysam)
- ("python-numpy" ,python2-numpy)
+ `(("python-cython" ,python-cython)
+ ("python-bx-python" ,python-bx-python)
+ ("python-pybigwig" ,python-pybigwig)
+ ("python-pysam" ,python-pysam)
+ ("python-numpy" ,python-numpy)
("zlib" ,zlib)))
(native-inputs
- `(("python-nose" ,python2-nose)))
+ `(("python-nose" ,python-nose)))
(home-page "http://rseqc.sourceforge.net/")
(synopsis "RNA-seq quality control package")
(description
(define-public star
(package
(name "star")
- (version "2.7.1a")
+ (version "2.7.3a")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/alexdobin/STAR.git")
(commit version)))
- (file-name (string-append name "-" version "-checkout"))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0n6g4s4hgw7qygs1z97j7a2dgz8gfaa4cv5pjvvvmarvk0x07hyg"))
+ "1hgiqw5qhs0pc1xazzihcfd92na02xyq2kb469z04y1v51kpvvjq"))
(modules '((guix build utils)))
(snippet
'(begin
(define-public taxtastic
(package
(name "taxtastic")
- (version "0.8.5")
+ (version "0.8.11")
(source (origin
- (method url-fetch)
- (uri (pypi-uri "taxtastic" version))
+ ;; The Pypi version does not include tests.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/fhcrc/taxtastic.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "03pysw79lsrvz4lwzis88j15067ffqbi4cid5pqhrlxmd6bh8rrk"))))
+ "1sv8mkg64jn7zdwf1jj71c16686yrwxk0apb1l8sjszy9p166g0p"))))
(build-system python-build-system)
(arguments
- `(#:python ,python-2
- #:phases
+ `(#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'prepare-directory
+ (lambda _
+ ;; The git checkout must be writable for tests.
+ (for-each make-file-writable (find-files "."))
+ ;; This test fails, but the error is not caught by the test
+ ;; framework, so the tests fail...
+ (substitute* "tests/test_taxit.py"
+ (("self.cmd_fails\\(''\\)")
+ "self.cmd_fails('nothing')"))
+ ;; This version file is expected to be created with git describe.
+ (mkdir-p "taxtastic/data")
+ (with-output-to-file "taxtastic/data/ver"
+ (lambda () (display ,version)))
+ #t))
+ (add-after 'unpack 'python37-compatibility
+ (lambda _
+ (substitute* "taxtastic/utils.py"
+ (("import csv") "import csv, errno")
+ (("os.errno") "errno"))
+ #t))
(replace 'check
- (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)))))
+ ;; Note, this fails to run with "-v" as it tries to write to a
+ ;; closed output stream.
+ (lambda _ (invoke "python" "-m" "unittest") #t)))))
(propagated-inputs
- `(("python-sqlalchemy" ,python2-sqlalchemy)
- ("python-decorator" ,python2-decorator)
- ("python-biopython" ,python2-biopython)
- ("python-pandas" ,python2-pandas)
- ("python-psycopg2" ,python2-psycopg2)
- ("python-fastalite" ,python2-fastalite)
- ("python-pyyaml" ,python2-pyyaml)
- ("python-six" ,python2-six)
- ("python-jinja2" ,python2-jinja2)
- ("python-dendropy" ,python2-dendropy)))
+ `(("python-sqlalchemy" ,python-sqlalchemy)
+ ("python-decorator" ,python-decorator)
+ ("python-biopython" ,python-biopython)
+ ("python-pandas" ,python-pandas)
+ ("python-psycopg2" ,python-psycopg2)
+ ("python-fastalite" ,python-fastalite)
+ ("python-pyyaml" ,python-pyyaml)
+ ("python-six" ,python-six)
+ ("python-jinja2" ,python-jinja2)
+ ("python-dendropy" ,python-dendropy)))
(home-page "https://github.com/fhcrc/taxtastic")
(synopsis "Tools for taxonomic naming and annotation")
(description
(define-public vcftools
(package
(name "vcftools")
- (version "0.1.15")
+ (version "0.1.16")
(source (origin
(method url-fetch)
(uri (string-append
version "/vcftools-" version ".tar.gz"))
(sha256
(base32
- "1qw30c45wihgy632rbz4rh3njnwj4msj46l1rsgdhyg6bgypmr1i"))))
+ "1qqlx7flfv7axrjwkaz6njkscsl1d0jw98ns8d8bh1n1hd1pgz6v"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no "check" target
(define-public infernal
(package
(name "infernal")
- (version "1.1.2")
+ (version "1.1.3")
(source (origin
(method url-fetch)
(uri (string-append "http://eddylab.org/software/infernal/"
"infernal-" version ".tar.gz"))
(sha256
(base32
- "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c"))))
+ "0pm8bm3s6nfa0av4x6m6h27lsg12b3lz3jm0fyh1mc77l2isd61v"))))
(build-system gnu-build-system)
(native-inputs
- `(("perl" ,perl))) ; for tests
+ `(("perl" ,perl)
+ ("python" ,python))) ; for tests
(home-page "http://eddylab.org/infernal/")
(synopsis "Inference of RNA alignments")
(description "Infernal (\"INFERence of RNA ALignment\") is a tool for
structure consensus, so in many cases, it is more capable of identifying RNA
homologs that conserve their secondary structure more than their primary
sequence.")
- ;; Infernal 1.1.2 requires VMX or SSE capability for parallel instructions.
+ ;; Infernal 1.1.3 requires VMX or SSE capability for parallel instructions.
(supported-systems '("i686-linux" "x86_64-linux"))
(license license:bsd-3)))
(define-public r-edger
(package
(name "r-edger")
- (version "3.28.0")
+ (version "3.28.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "1m7l6fbyik1b79v0h9qkmpa39svij1yiw24gxahbdqjg7fzsavh3"))))
+ "07dv99kl7jfa62nzcq705r56gcpb1hq7p4px48j71y2ddi1rqmr6"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-rsamtools
(package
(name "r-rsamtools")
- (version "2.2.2")
+ (version "2.2.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Rsamtools" version))
(sha256
(base32
- "1larx1a9cngmcsm2n7yyxrlnk69zi8m9dp3b90jva0ynspyi76v7"))))
+ "1vj43acawqqkf9yval9fzxarpsf04fmn78m2hq4f083w1k0myhyr"))))
(properties
`((upstream-name . "Rsamtools")))
(build-system r-build-system)
(define-public r-qtl
(package
(name "r-qtl")
- (version "1.45-11")
+ (version "1.46-2")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "1d6qgj602fm6zia3djl4hmca0ri4v57ffp3g93p2yc3cabx2hq90"))))
+ "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))
(build-system r-build-system)
(home-page "https://rqtl.org/")
(synopsis "R package for analyzing QTL experiments in genetics")
(define-public r-rhtslib
(package
(name "r-rhtslib")
- (version "1.18.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhtslib" version))
(sha256
(base32
- "04inkq44lxwymqv51mxgaphasqjcdc9rl5p58imnrdm0kszs8prm"))))
+ "0gkbrmrcg55c9s5166ifljlx0v25rv4ijdyp4wf4c292xd6chy2l"))))
(properties `((upstream-name . "Rhtslib")))
(build-system r-build-system)
;; Without this a temporary directory ends up in the Rhtslib.so binary,
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-zlibbioc" ,r-zlibbioc)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr))) ; for vignettes
(inputs
`(("zlib" ,zlib)))
(home-page "https://github.com/al2na/methylKit")
(define-public r-seqminer
(package
(name "r-seqminer")
- (version "7.1")
+ (version "8.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "seqminer" version))
(sha256
(base32
- "1jydcpkw4rwfp983j83kipvsvr10as9pb49zzn3c2v09k1gh3ymy"))))
+ "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
("r-ggplot2" ,r-ggplot2)
("r-lattice" ,r-lattice)
("r-limma" ,r-limma)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr))) ; for vignettes
(home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
(synopsis "Variance stabilization and calibration for microarray data")
(description
(define-public r-seurat
(package
(name "r-seurat")
- (version "3.1.3")
+ (version "3.1.4")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
- "0962mfgqk1di3wy1j0xdkvnw0q5m3q4xzd67d1l6dijlqiz8nfal"))))
+ "0lhjbjhv1hnx5i3gkx41k68i8ykay3f24708h30wx9xywww9lsvi"))))
(properties `((upstream-name . "Seurat")))
(build-system r-build-system)
(propagated-inputs
("r-mass" ,r-mass)
("r-matrix" ,r-matrix)
("r-metap" ,r-metap)
+ ("r-patchwork" ,r-patchwork)
("r-pbapply" ,r-pbapply)
("r-plotly" ,r-plotly)
("r-png" ,r-png)
(define-public r-gviz
(package
(name "r-gviz")
- (version "1.30.1")
+ (version "1.30.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Gviz" version))
(sha256
(base32
- "03jj193fzmhvkjw8f5zk6wgflkvm3phny0q38scawcplfsyb8z64"))))
+ "0c9i26h5czm60n1bxzmdxxpywcj0sig6wcj913pb41mr83bbgra3"))))
(properties `((upstream-name . "Gviz")))
(build-system r-build-system)
(propagated-inputs
(define-public r-hdf5array
(package
(name "r-hdf5array")
- (version "1.14.1")
+ (version "1.14.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HDF5Array" version))
(sha256
(base32
- "04hd02zd5jix5p2zg10asmwjg1fynqgmclbhbmk7fb6arx5hm11f"))))
+ "1z153a7nxmlml72pl1saasj2il9g5ahpynkpv3mkhhsvl5kbwbh6"))))
(properties `((upstream-name . "HDF5Array")))
(build-system r-build-system)
(inputs
(define-public r-scran
(package
(name "r-scran")
- (version "1.14.5")
+ (version "1.14.6")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scran" version))
(sha256
(base32
- "0ydy6gvpgpvrs4ryk1qvmmxp6cpaizs294jwg42jawxndkds1l3y"))))
+ "1y8wlgk5zbv7c7gcp0ahfpbh9lifab7y3zwf0093fzaw7vr1y6cr"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
matplotlib.use('Agg')
" line)))
;; Make sure GESS has all modules in its path
- (wrap-program (string-append target "GESS.py")
- `("PYTHONPATH" ":" prefix (,target ,(getenv "PYTHONPATH"))))
+ (wrap-script (string-append target "GESS.py")
+ `("PYTHONPATH" ":" = (,target ,(getenv "PYTHONPATH"))))
(mkdir-p bin)
(symlink (string-append target "GESS.py")
(string-append bin "GESS.py"))
("python2-scipy" ,python2-scipy)
("python2-numpy" ,python2-numpy)
("python2-networkx" ,python2-networkx)
- ("python2-biopython" ,python2-biopython)))
+ ("python2-biopython" ,python2-biopython)
+ ("guile" ,guile-3.0))) ; for the script wrapper
(home-page "https://compbio.uthscsa.edu/GESS_Web/")
(synopsis "Detect exon-skipping events from raw RNA-seq data")
(description
single-cell RNA-seq data.")
(license license:bsd-3)))
-;; pigx-scrnaseq does not work with the latest version of loompy.
-(define-public python-loompy-for-pigx-scrnaseq
- (package (inherit python-loompy)
- (name "python-loompy")
- (version "2.0.3")
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/linnarsson-lab/loompy.git")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0pjyl532pl8sbv71yci6h0agchn0naw2qjcwj50n6afrsahbsag3"))))
- ;; There are none.
- (arguments '(#:tests? #f))))
-
;; We cannot use the latest commit because it requires Java 9.
(define-public java-forester
(let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6")
(version "1.005")
(source (origin
(method url-fetch)
- (uri (string-append "http://search.maven.org/remotecontent?"
- "filepath=org/biojava/thirdparty/forester/"
+ (uri (string-append "https://repo1.maven.org/maven2/"
+ "org/biojava/thirdparty/forester/"
version "/forester-" version "-sources.jar"))
(file-name (string-append name "-" version ".jar"))
(sha256
(method url-fetch)
(uri (string-append "https://raw.githubusercontent.com/cmzmasek/forester/"
"29e04321615da6b35c1e15c60e52caf3f21d8e6a/"
- "forester/java/classes/resources/synth_look_and_feel_1.xml"))
+ "forester/java/classes/resources/"
+ "synth_look_and_feel_1.xml"))
(file-name (string-append name "-synth-look-and-feel-" version ".xml"))
(sha256
(base32
(define-public pigx-scrnaseq
(package
(name "pigx-scrnaseq")
- (version "0.0.8")
+ (version "1.1.4")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
"/pigx_scrnaseq-" version ".tar.gz"))
(sha256
(base32
- "0zv0sc5amivxhb95vx2gfx6l9bh7n80fh7h47dalnwxxnfvnzai4"))))
+ "1d5l3gywypi67yz9advxq5xkgfhr4733gj0bwnngm723i3hdf5w9"))))
(build-system gnu-build-system)
- (arguments
- `(#:configure-flags
- (list (string-append "PICARDJAR=" (assoc-ref %build-inputs "java-picard")
- "/share/java/picard.jar")
- (string-append "DROPSEQJAR=" (assoc-ref %build-inputs "dropseq-tools")
- "/share/java/dropseq.jar"))))
(inputs
`(("coreutils" ,coreutils)
("perl" ,perl)
- ("dropseq-tools" ,dropseq-tools)
("fastqc" ,fastqc)
- ("java-picard" ,java-picard-2.10.3) ; same as for dropseq
+ ("flexbar" ,flexbar)
("java" ,icedtea-8)
+ ("jellyfish" ,jellyfish)
("python-wrapper" ,python-wrapper)
("python-pyyaml" ,python-pyyaml)
("python-pandas" ,python-pandas)
("python-magic" ,python-magic)
("python-numpy" ,python-numpy)
- ("python-loompy" ,python-loompy-for-pigx-scrnaseq)
+ ("python-loompy" ,python-loompy)
("ghc-pandoc" ,ghc-pandoc)
("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
("samtools" ,samtools)
("r-rtsne" ,r-rtsne)
("r-scater" ,r-scater)
("r-scran" ,r-scran)
+ ("r-seurat" ,r-seurat)
("r-singlecellexperiment" ,r-singlecellexperiment)
("r-stringr" ,r-stringr)
("r-yaml" ,r-yaml)))
(define-public python-scanpy
(package
(name "python-scanpy")
- (version "1.4")
- ;; Fetch from git because the pypi tarball does not include tests.
+ (version "1.4.5.1")
(source
(origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/theislab/scanpy.git")
- (commit version)))
- (file-name (git-file-name name version))
+ (method url-fetch)
+ (uri (pypi-uri "scanpy" version))
(sha256
(base32
- "0zn6x6c0cnm1a20i6isigwb51g3pr9zpjk8r1minjqnxi5yc9pm4"))))
+ "14kh1ji70xxhmri5q8sgcibsidhr6f221wxrcw8a5xvibj5da17j"))))
(build-system python-build-system)
(arguments
`(#:phases
("python-igraph" ,python-igraph)
("python-joblib" ,python-joblib)
("python-louvain" ,python-louvain)
+ ("python-legacy-api-wrap" ,python-legacy-api-wrap)
("python-matplotlib" ,python-matplotlib)
("python-natsort" ,python-natsort)
("python-networkx" ,python-networkx)
("python-numba" ,python-numba)
+ ("python-packaging" ,python-packaging)
("python-pandas" ,python-pandas)
+ ("python-patsy" ,python-patsy)
("python-scikit-learn" ,python-scikit-learn)
("python-scipy" ,python-scipy)
("python-seaborn" ,python-seaborn)
("python-statsmodels" ,python-statsmodels)
- ("python-tables" ,python-tables)))
+ ("python-tables" ,python-tables)
+ ("python-umap-learn" ,python-umap-learn)))
(native-inputs
- `(("python-pytest" ,python-pytest)))
+ `(("python-pytest" ,python-pytest)
+ ("python-setuptools-scm" ,python-setuptools-scm)))
(home-page "https://github.com/theislab/scanpy")
(synopsis "Single-Cell Analysis in Python.")
(description "Scanpy is a scalable toolkit for analyzing single-cell gene
(define-public python-pyfaidx
(package
(name "python-pyfaidx")
- (version "0.5.7")
+ (version "0.5.8")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyfaidx" version))
(sha256
(base32
- "02jvdx3ksy6w5gd29i1d0g0zsabbz7c14qg482ff7pza6sdl0b2i"))))
+ "038xi3a6zvrxbyyfpp64ka8pcjgsdq4fgw9cl5lpxbvmm1bzzw2q"))))
(build-system python-build-system)
(propagated-inputs
`(("python-six" ,python-six)))
fasta subsequences.")
(license license:bsd-3)))
+(define-public python2-pyfaidx
+ (package-with-python2 python-pyfaidx))
+
(define-public python-cooler
(package
(name "python-cooler")
(define-public jamm
(package
(name "jamm")
- (version "1.0.7.5")
+ (version "1.0.7.6")
(source
(origin
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32
- "0ls889jcma1ch9h21jjhnkadgszgqj41842hhcjh6cg88f85qf3i"))))
+ "0bsa5mf9n9q5jz7mmacrra41l7r8rac5vgsn6wv1fb52ya58b970"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are none
(define-public ngless
(package
(name "ngless")
- (version "1.0.1")
+ (version "1.1.0")
(source
(origin
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32
- "06ygv8q2zjqsnrid1302yrlhhvb8ik48nq6n0higk3i1mdc8r0dg"))))
+ "1wim8wpqyff080dfcazynrmjwqas38m24m0v350w245mmhrapdma"))))
(build-system haskell-build-system)
(arguments
`(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1:
(base32
"0fgygyzqgrq32dv6a00biq1p1cwi6kbl5iqblxq1kklj6b2mzmhs"))))
(build-system python-build-system)
+ (native-inputs
+ `(("python-joblib" ,python-joblib)))
(propagated-inputs
`(("python-click" ,python-click)
("python-cython" ,python-cython)
HCoop / jackhill / guix / guix.git / blobdiff