(define-public blast+
(package
(name "blast+")
- (version "2.6.0")
+ (version "2.7.1")
(source (origin
(method url-fetch)
(uri (string-append
version "/ncbi-blast-" version "+-src.tar.gz"))
(sha256
(base32
- "15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405"))
- (patches (search-patches "blast+-fix-makefile.patch"))
+ "1jlq0afxxgczpp35k6mxh8mn4jzq7vqcnaixk166sfj10wq8v9qh"))
(modules '((guix build utils)))
(snippet
'(begin
"include")) ; 33 MB
(inputs
`(("bzip2" ,bzip2)
+ ("lmdb" ,lmdb)
("zlib" ,zlib)
("pcre" ,pcre)
("perl" ,perl)
`(#:tests? #f ; there are no tests
#:make-flags
;; Executables are copied directly to the PREFIX.
- (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin"))
+ (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin")
+ ;; Support longer sequences (e.g. Pacbio sequences)
+ "MAX_SEQ=60000000")
#:phases
(modify-phases %standard-phases
;; No "configure" script
(define-public r-dexseq
(package
(name "r-dexseq")
- (version "1.28.1")
+ (version "1.28.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DEXSeq" version))
(sha256
(base32
- "0g5w9bn2nb3m670hkcsnhfvvkza2318z9irlhhwhb3n8rdzlsdym"))))
+ "134znafy7hn38rp4nia4pglz56fz6nbkxrf7z2k1sajfsgxa1hs6"))))
(properties `((upstream-name . "DEXSeq")))
(build-system r-build-system)
(propagated-inputs
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.18.1")
+ (version "1.18.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "049pyzr8iszv3g7wdqf3pz7vg7bzd450c20ln6fgw4g5xnkkr10s"))))
+ "07bm35jcczpyxap0b3gky4b28z38z423sngzsm19d9krjxr76b5p"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
(define-public r-variantannotation
(package
(name "r-variantannotation")
- (version "1.28.10")
+ (version "1.28.11")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "VariantAnnotation" version))
(sha256
(base32
- "0kxf583cgkdz1shi85r0mpnfxmzi7s5f6srd1czbdl2iibvrm8jn"))))
+ "19bxi5b9fzqdjadb8bfm8xsgi6nvrwbgn1xcpk59bnmv9vzjkwrh"))))
(properties
`((upstream-name . "VariantAnnotation")))
(inputs
(define-public r-biocparallel
(package
(name "r-biocparallel")
- (version "1.16.5")
+ (version "1.16.6")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocParallel" version))
(sha256
(base32
- "1164dk0fajb2vrkfpcjs11055qf1cs4vvbnq0aqdaaf2p4lyx41l"))))
+ "1iv2xzm6lz371z0llhcxl8hmc5jfw0hjwnf1qc8d7jk9djgcaks2"))))
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
(define-public r-rsamtools
(package
(name "r-rsamtools")
- (version "1.34.0")
+ (version "1.34.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Rsamtools" version))
(sha256
(base32
- "01v4bjhj2i126pwyk0v9lvmfp2ih495xsq903k3xa2z24bjxphbi"))))
+ "02paq7klabdkaf1b8pmmbpmyqsj3yncnfsz62rgka6r4dpsilwk9"))))
(properties
`((upstream-name . "Rsamtools")))
(build-system r-build-system)
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.42.1")
+ (version "1.42.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "1ycmcxvgvszvjv75hlmg0i6pq8i7r8720vgmfayb905s9l6j82x6"))))
+ "1c76g6h9lx2nm7dvb2zp9dmrpk3vanx3zaz6q9clggpj7yj5lmjd"))))
(build-system r-build-system)
(arguments
`(#:phases
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.34.2")
+ (version "1.34.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "0qs94b0ywrjyc9m1jykrbch3lb07576m508dikvx18vwn304mban"))))
+ "09gc1vbqszrr3ixv4hsfan2l18fcf3gg58783mrfwjv6ci9c4w0d"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
downloaded from Encode.")
(license license:gpl3+)))
-(define-public r-org-hs-eg-db
- (package
- (name "r-org-hs-eg-db")
- (version "3.7.0")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "org.Hs.eg.db_" version ".tar.gz"))
- (sha256
- (base32
- "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
- (properties
- `((upstream-name . "org.Hs.eg.db")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
- (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
- (synopsis "Genome wide annotation for Human")
- (description
- "This package contains genome-wide annotations for Human, primarily based
-on mapping using Entrez Gene identifiers.")
- (license license:artistic2.0)))
-
-(define-public r-org-ce-eg-db
- (package
- (name "r-org-ce-eg-db")
- (version "3.7.0")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "org.Ce.eg.db_" version ".tar.gz"))
- (sha256
- (base32
- "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
- (properties
- `((upstream-name . "org.Ce.eg.db")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
- (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
- (synopsis "Genome wide annotation for Worm")
- (description
- "This package provides mappings from Entrez gene identifiers to various
-annotations for the genome of the model worm Caenorhabditis elegans.")
- (license license:artistic2.0)))
-
-(define-public r-org-dm-eg-db
- (package
- (name "r-org-dm-eg-db")
- (version "3.7.0")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "org.Dm.eg.db_" version ".tar.gz"))
- (sha256
- (base32
- "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
- (properties
- `((upstream-name . "org.Dm.eg.db")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
- (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
- (synopsis "Genome wide annotation for Fly")
- (description
- "This package provides mappings from Entrez gene identifiers to various
-annotations for the genome of the model fruit fly Drosophila melanogaster.")
- (license license:artistic2.0)))
-
-(define-public r-org-mm-eg-db
- (package
- (name "r-org-mm-eg-db")
- (version "3.7.0")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "org.Mm.eg.db_" version ".tar.gz"))
- (sha256
- (base32
- "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
- (properties
- `((upstream-name . "org.Mm.eg.db")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
- (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
- (synopsis "Genome wide annotation for Mouse")
- (description
- "This package provides mappings from Entrez gene identifiers to various
-annotations for the genome of the model mouse Mus musculus.")
- (license license:artistic2.0)))
-
(define-public r-seqlogo
(package
(name "r-seqlogo")
Stephens (1990).")
(license license:lgpl2.0+)))
-(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
- (package
- (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
- (version "3.4.4")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "TxDb.Mmusculus.UCSC.mm10.knownGene_"
- version ".tar.gz"))
- (sha256
- (base32
- "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
- (properties
- `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
- (build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
- (propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-annotationdbi" ,r-annotationdbi)))
- (home-page
- "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
- (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
- (description
- "This package loads a TxDb object, which is an R interface to
-prefabricated databases contained in this package. This package provides
-the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
-based on the knownGene track.")
- (license license:artistic2.0)))
-
-(define-public r-bsgenome-celegans-ucsc-ce6
- (package
- (name "r-bsgenome-celegans-ucsc-ce6")
- (version "1.4.0")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Celegans.UCSC.ce6_"
- version ".tar.gz"))
- (sha256
- (base32
- "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
- (properties
- `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
- (build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
- (propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
- (home-page
- "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
- (synopsis "Full genome sequences for Worm")
- (description
- "This package provides full genome sequences for Caenorhabditis
-elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
-objects.")
- (license license:artistic2.0)))
-
-(define-public r-bsgenome-celegans-ucsc-ce10
- (package
- (name "r-bsgenome-celegans-ucsc-ce10")
- (version "1.4.0")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Celegans.UCSC.ce10_"
- version ".tar.gz"))
- (sha256
- (base32
- "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
- (properties
- `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
- (build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
- (propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
- (home-page
- "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
- (synopsis "Full genome sequences for Worm")
- (description
- "This package provides full genome sequences for Caenorhabditis
-elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
-objects.")
- (license license:artistic2.0)))
-
-(define-public r-bsgenome-dmelanogaster-ucsc-dm3
- (package
- (name "r-bsgenome-dmelanogaster-ucsc-dm3")
- (version "1.4.0")
- (source (origin
- (method url-fetch)
- ;; We cannot use bioconductor-uri here because this tarball is
- ;; located under "data/annotation/" instead of "bioc/".
- (uri (string-append "https://www.bioconductor.org/packages/"
- "release/data/annotation/src/contrib/"
- "BSgenome.Dmelanogaster.UCSC.dm3_"
- version ".tar.gz"))
- (sha256
- (base32
- "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
- (properties
- `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
- (build-system r-build-system)
- ;; As this package provides little more than a very large data file it
- ;; doesn't make sense to build substitutes.
- (arguments `(#:substitutable? #f))
- (propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
- (home-page
- "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
- (synopsis "Full genome sequences for Fly")
- (description
- "This package provides full genome sequences for Drosophila
-melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
-Biostrings objects.")
- (license license:artistic2.0)))
-
(define-public r-motifrg
(package
(name "r-motifrg")
(define-public r-rhtslib
(package
(name "r-rhtslib")
- (version "1.14.0")
+ (version "1.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rhtslib" version))
(sha256
(base32
- "1h4q54f8za3aaxgy186zf2165sar5c3cgxkk44lq5hzx5pxkl5wn"))))
+ "13fv78sk5g0gqfl3ks3rps3zc1k66a4lzxvgn36r7ix43yxk7hnr"))))
(properties `((upstream-name . "Rhtslib")))
(build-system r-build-system)
(propagated-inputs
(define-public r-mzr
(package
(name "r-mzr")
- (version "2.16.1")
+ (version "2.16.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mzR" version))
(sha256
(base32
- "0mlwg646k49klxrznckzfv54a9mz6irj42fqpaaa0xjm6cw2lwaa"))
+ "19fn58zl59kd0hsjjc6y975y9187nfls0028a4k3v0s9wfg5b3vn"))
(modules '((guix build utils)))
(snippet
'(begin
-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
#t)))))
(inputs
- `(("boost" ,boost) ; use this instead of the bundled boost sources
+ `(;; XXX Boost 1.69 will not work here.
+ ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
("zlib" ,zlib)))
(propagated-inputs
`(("r-biobase" ,r-biobase)
(define-public r-annotationhub
(package
(name "r-annotationhub")
- (version "2.14.2")
+ (version "2.14.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationHub" version))
(sha256
(base32
- "17fgrvcnbii9siv5rq5j09bxhqffx47f6jf10418qvr7hh61ic1g"))))
+ "18v2mk395svq3c19wzi6bjwjfnmrvjqkzmj7cmaji7rx4xdgz6ck"))))
(properties `((upstream-name . "AnnotationHub")))
(build-system r-build-system)
(propagated-inputs
(define-public r-ensembldb
(package
(name "r-ensembldb")
- (version "2.6.3")
+ (version "2.6.7")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ensembldb" version))
(sha256
(base32
- "0kzdsfk6mdwlp57sw4j2cf7lx5nc67v5j0xr3iag9kzmgikaq1lb"))))
+ "1wqq0m1fgvgkzq5zr2s9cj2s7qkg9lx3dwwsqixzs5fn52p4dn7f"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
(define-public r-gviz
(package
(name "r-gviz")
- (version "1.26.4")
+ (version "1.26.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Gviz" version))
(sha256
(base32
- "0jvcivgw0ahv2rjadxmrww76xambhf7silczmh38nn4yn4qw6w9y"))))
+ "1dpkcaar7qgzg3vgafvkplprhwmhzpb7ph009kr6ajm36hx4z81c"))))
(properties `((upstream-name . "Gviz")))
(build-system r-build-system)
(propagated-inputs
HCoop / jackhill / guix / guix.git / blobdiff