From 77bea84ba128ac2c7d55530d2c581021e8d16884 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 9 Nov 2018 19:00:23 +0100 Subject: gnu: r-biocviews: Update to 1.50.5. * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.5. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8820ba0d8e..9147a9866b 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) -- cgit v1.2.3 From 88514b912427691272650195ad1941f7ead1ac36 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 9 Nov 2018 19:00:33 +0100 Subject: gnu: r-biostrings: Update to 2.50.1. * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9147a9866b..3b1b9c2c96 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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) -- cgit v1.2.3 From 03a415365a1cfcc263f56d309f33a1a581790ca7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 9 Nov 2018 19:00:42 +0100 Subject: gnu: r-ensembldb: Update to 2.6.1. * gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3b1b9c2c96..55631530ca 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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) -- cgit v1.2.3 From 5f9b38ba3438c7bba9203757391c256507573b7b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 11 Nov 2018 23:12:32 +0100 Subject: gnu: r-s4vectors: Update to 0.20.1. * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 55631530ca..bf49f4e1dc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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) -- cgit v1.2.3 From 13a574652bf2f9843b37a9ec6ae2c9204a3662b4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Nov 2018 23:27:06 +0100 Subject: gnu: r-genomeinfodbdata: Update to 1.2.0. * gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bf49f4e1dc..f48b6bd0e3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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) -- cgit v1.2.3 From 13e70f6304e9b13bdadc15bff33357f44173fe89 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Nov 2018 23:27:24 +0100 Subject: gnu: r-go-db: Update to 3.7.0. * gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f48b6bd0e3..2b3fc0acd8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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) -- cgit v1.2.3 From cb9e6ed7029a546202f6ddebe49aafd9287ff85a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Nov 2018 23:27:36 +0100 Subject: gnu: r-genomationdata: Update to 1.14.0. * gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2b3fc0acd8..7101f28ba0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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. -- cgit v1.2.3 From fc7683fa30035221612d883dea82413c048f3454 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Nov 2018 23:27:49 +0100 Subject: gnu: r-org-hs-eg-db: Update to 3.7.0. * gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7101f28ba0..b7f1970ad5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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) -- cgit v1.2.3 From 76bd16bcf6e42e3192b8aaefce26cef56d8bfc40 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Nov 2018 23:28:05 +0100 Subject: gnu: r-org-ce-eg-db: Update to 3.7.0. * gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b7f1970ad5..fe61fc601e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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) -- cgit v1.2.3 From 314511b86273ff1cb61a476cdb825f80b96dde0b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Nov 2018 23:28:19 +0100 Subject: gnu: r-org-dm-eg-db: Update to 3.7.0. * gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fe61fc601e..a4402b2737 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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) -- cgit v1.2.3 From d34959b8d4f4f20b3110fa6d6c54fa6f755a7a7c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Nov 2018 23:28:33 +0100 Subject: gnu: r-org-mm-eg-db: Update to 3.7.0. * gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a4402b2737..a1d87fc686 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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) -- cgit v1.2.3 From 51b262f3109fe8aba112b7cc49521c5c6810ce54 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Nov 2018 23:28:46 +0100 Subject: gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4. * gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): Update to 3.4.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a1d87fc686..674bbb107d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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) -- cgit v1.2.3 From ee66a13563dc0ca03865ec3d3d36f8c55e885ac0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 14 Nov 2018 13:56:54 +0100 Subject: gnu: Add jamm. * gnu/packages/bioinformatics.scm (jamm): New variable. --- gnu/packages/bioinformatics.scm | 79 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 79 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 674bbb107d..58cee5cbbe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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") -- cgit v1.2.3