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-rw-r--r--gnu/packages/bioinformatics.scm127
1 files changed, 103 insertions, 24 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8820ba0d8e..58cee5cbbe 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7099,13 +7099,13 @@ Bioconductor, CRAN, and Github.")
(define-public r-biocviews
(package
(name "r-biocviews")
- (version "1.50.1")
+ (version "1.50.5")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "0hjm3r58i0r9qhyar9pk250cx7sfijg0lnvi12a9s6brmmbip1a3"))))
+ "0rc1n89n04ylvy9gvsgvizcs77bh70jg1nkjjsjs7rqbr3zzdysz"))))
(properties
`((upstream-name . "biocViews")))
(build-system r-build-system)
@@ -7268,13 +7268,13 @@ abnormal copy number.")
(define-public r-s4vectors
(package
(name "r-s4vectors")
- (version "0.20.0")
+ (version "0.20.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
- "0qgiykjhnsvvpcp3zwmrnpx3bv3msvj0szchyvb1yb0fxw716xc5"))))
+ "18whrw67nxn82xshckl2pjy7d14sa3c27h3n9naqyqwz88lr6dzg"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
@@ -7349,7 +7349,7 @@ possible.")
(define-public r-genomeinfodbdata
(package
(name "r-genomeinfodbdata")
- (version "1.1.0")
+ (version "1.2.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
@@ -7359,7 +7359,7 @@ possible.")
version ".tar.gz"))
(sha256
(base32
- "0k1hsjx6n2i1sf14hyrgdhxqxm5mxk0bgnivhiax944whcicmzbf"))))
+ "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
(properties
`((upstream-name . "GenomeInfoDbData")))
(build-system r-build-system)
@@ -7657,13 +7657,13 @@ objects.")
(define-public r-biostrings
(package
(name "r-biostrings")
- (version "2.50.0")
+ (version "2.50.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biostrings" version))
(sha256
(base32
- "0zw0dj67fnpbz4iqnam5fxs92c1c8w8d7mzl0rkq4ksx0xl8vgg7"))))
+ "1qyv1ps7vy6gy78pm2rcikg0bgf1mv7falahjp3pkwqq1272hrl8"))))
(properties
`((upstream-name . "Biostrings")))
(build-system r-build-system)
@@ -7910,7 +7910,7 @@ extracting the desired features in a convenient format.")
(define-public r-go-db
(package
(name "r-go-db")
- (version "3.6.0")
+ (version "3.7.0")
(source (origin
(method url-fetch)
(uri (string-append "https://www.bioconductor.org/packages/"
@@ -7918,7 +7918,7 @@ extracting the desired features in a convenient format.")
version ".tar.gz"))
(sha256
(base32
- "0fi2qywr9apg5lwfqfq9qq6bgrnv4rdhxx25656qn4bsy62i838j"))))
+ "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
(properties
`((upstream-name . "GO.db")))
(build-system r-build-system)
@@ -8121,7 +8121,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
(define-public r-genomationdata
(package
(name "r-genomationdata")
- (version "1.10.0")
+ (version "1.14.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
@@ -8131,7 +8131,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
"genomationData_" version ".tar.gz"))
(sha256
(base32
- "0h7g5x3kyb50qlblz5hc85lfm6n6f5nb68i146way3ggs04sqvla"))))
+ "10xyb8akjrhmak2i0mnv1agny2ipy364q9nlibyplpzc7vdb6bw7"))))
(build-system r-build-system)
;; As this package provides little more than large data files, it doesn't
;; make sense to build substitutes.
@@ -8149,7 +8149,7 @@ downloaded from Encode.")
(define-public r-org-hs-eg-db
(package
(name "r-org-hs-eg-db")
- (version "3.5.0")
+ (version "3.7.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
@@ -8159,7 +8159,7 @@ downloaded from Encode.")
"org.Hs.eg.db_" version ".tar.gz"))
(sha256
(base32
- "1v6wa5613cjq59xd7x1qz8lr9nb2abm9abl2cci1khrnrlpla927"))))
+ "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
(properties
`((upstream-name . "org.Hs.eg.db")))
(build-system r-build-system)
@@ -8175,7 +8175,7 @@ on mapping using Entrez Gene identifiers.")
(define-public r-org-ce-eg-db
(package
(name "r-org-ce-eg-db")
- (version "3.5.0")
+ (version "3.7.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
@@ -8185,7 +8185,7 @@ on mapping using Entrez Gene identifiers.")
"org.Ce.eg.db_" version ".tar.gz"))
(sha256
(base32
- "02ggchixlmzywhsbr0h2ms4dravv7m5964cjxqcjxqs16vjwlbk9"))))
+ "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
(properties
`((upstream-name . "org.Ce.eg.db")))
(build-system r-build-system)
@@ -8201,7 +8201,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.")
(define-public r-org-dm-eg-db
(package
(name "r-org-dm-eg-db")
- (version "3.5.0")
+ (version "3.7.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
@@ -8211,7 +8211,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.")
"org.Dm.eg.db_" version ".tar.gz"))
(sha256
(base32
- "033qak1d3wwz17va0bh8z8p8arx0aw2va6gm1qfwsvdkj9cd9d7d"))))
+ "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
(properties
`((upstream-name . "org.Dm.eg.db")))
(build-system r-build-system)
@@ -8227,7 +8227,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.")
(define-public r-org-mm-eg-db
(package
(name "r-org-mm-eg-db")
- (version "3.5.0")
+ (version "3.7.0")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
@@ -8237,7 +8237,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.")
"org.Mm.eg.db_" version ".tar.gz"))
(sha256
(base32
- "11q21p3ki4bn4hb3aix0g775l45l66jmas6m94nfhqqnpjhv4d6g"))))
+ "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
(properties
`((upstream-name . "org.Mm.eg.db")))
(build-system r-build-system)
@@ -8368,7 +8368,7 @@ in Biostrings objects.")
(define-public r-txdb-mmusculus-ucsc-mm10-knowngene
(package
(name "r-txdb-mmusculus-ucsc-mm10-knowngene")
- (version "3.4.0")
+ (version "3.4.4")
(source (origin
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
@@ -8379,7 +8379,7 @@ in Biostrings objects.")
version ".tar.gz"))
(sha256
(base32
- "08gava9wsvpcqz51k2sni3pj03n5155v32d9riqbf305nbirqbkb"))))
+ "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
(properties
`((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
(build-system r-build-system)
@@ -10215,14 +10215,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
(define-public r-ensembldb
(package
(name "r-ensembldb")
- (version "2.6.0")
+ (version "2.6.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ensembldb" version))
(sha256
(base32
- "12jqz9h6w4mxyfr43w5qbwmacn512aw0mnl0zvhsg5i7p4qj45ks"))))
+ "1js05dcv1dj4g2vj7lzlg0rgjcjlk2irdr9rxqpwxmivm8nbvf36"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
@@ -14118,6 +14118,85 @@ enrichment analysis (GSEA) calculation with or without the absolute filtering.
absolute GSEA.")
(license license:gpl2)))
+(define-public jamm
+ (package
+ (name "jamm")
+ (version "1.0.7.5")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mahmoudibrahim/JAMM.git")
+ (commit (string-append "JAMMv" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0ls889jcma1ch9h21jjhnkadgszgqj41842hhcjh6cg88f85qf3i"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are none
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'build
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (substitute* "JAMM.sh"
+ (("^sPath=.*")
+ (string-append "")))
+ #t))
+ (replace 'install
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (libexec (string-append out "/libexec/jamm"))
+ (bin (string-append out "/bin")))
+ (substitute* '("JAMM.sh"
+ "SignalGenerator.sh")
+ (("^sPath=.*")
+ (string-append "sPath=\"" libexec "\"\n")))
+ (for-each (lambda (file)
+ (install-file file libexec))
+ (list "bincalculator.r"
+ "peakfinder.r"
+ "peakhelper.r"
+ "signalmaker.r"
+ "xcorr.r"
+ "xcorrhelper.r"
+ ;; Perl scripts
+ "peakfilter.pl"
+ "readshifter.pl"))
+
+ (for-each
+ (lambda (script)
+ (chmod script #o555)
+ (install-file script bin)
+ (wrap-program (string-append bin "/" script)
+ `("PATH" ":" prefix
+ (,(string-append (assoc-ref inputs "coreutils") "/bin")
+ ,(string-append (assoc-ref inputs "gawk") "/bin")
+ ,(string-append (assoc-ref inputs "perl") "/bin")
+ ,(string-append (assoc-ref inputs "r-minimal") "/bin")))
+ `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")))
+ `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE")))))
+ (list "JAMM.sh" "SignalGenerator.sh")))
+ #t)))))
+ (inputs
+ `(("bash" ,bash)
+ ("coreutils" ,coreutils)
+ ("gawk" ,gawk)
+ ("perl" ,perl)
+ ("r-minimal" ,r-minimal)
+ ;;("r-parallel" ,r-parallel)
+ ("r-signal" ,r-signal)
+ ("r-mclust" ,r-mclust)))
+ (home-page "https://github.com/mahmoudibrahim/JAMM")
+ (synopsis "Peak finder for NGS datasets")
+ (description
+ "JAMM is a peak finder for next generation sequencing datasets (ChIP-Seq,
+ATAC-Seq, DNase-Seq, etc.) that can integrate replicates and assign peak
+boundaries accurately. JAMM is applicable to both broad and narrow
+datasets.")
+ (license license:gpl3+)))
+
(define-public ngless
(package
(name "ngless")
generated by cgit v1.2.3 (git 2.25.4) at 2024-11-07 22:42:04 +0000