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-rw-r--r--gnu/packages/bioinformatics.scm88
1 files changed, 39 insertions, 49 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 281bd1f427..0afc0a6979 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4,6 +4,7 @@
;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -2507,16 +2508,13 @@ interrupted by stop codons. OrfM finds and prints these ORFs.")
(define-public python2-pbcore
(package
(name "python2-pbcore")
- (version "0.9.3")
+ (version "1.2.8")
(source (origin
(method url-fetch)
- (uri (string-append
- "https://github.com/PacificBiosciences/pbcore/archive/"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (uri (pypi-uri "pbcore" version))
(sha256
(base32
- "1z46rwjac93jm87cbj2zgjg6qvsgs65140wkbbxsvxps7ai4pm09"))))
+ "02pfn5raa3zf739672bg0dkx7z3j2c4nx7vmpfjqy5b12jrqpymk"))))
(build-system python-build-system)
(arguments `(#:python ,python-2)) ; pbcore requires Python 2.7
(inputs
@@ -2525,7 +2523,10 @@ interrupted by stop codons. OrfM finds and prints these ORFs.")
("python-pysam" ,python2-pysam)
("python-h5py" ,python2-h5py)))
(native-inputs
- `(("python-setuptools" ,python2-setuptools)))
+ `(("python-docutils" ,python2-docutils)
+ ("python-nose" ,python2-nose)
+ ("python-setuptools" ,python2-setuptools)
+ ("python-sphinx" ,python2-sphinx)))
(home-page "http://pacificbiosciences.github.io/pbcore/")
(synopsis "Library for reading and writing PacBio data files")
(description
@@ -3691,15 +3692,15 @@ Cuffdiff or Ballgown programs.")
(define-public vcftools
(package
(name "vcftools")
- (version "0.1.12b")
+ (version "0.1.14")
(source (origin
(method url-fetch)
(uri (string-append
- "mirror://sourceforge/vcftools/vcftools_"
- version ".tar.gz"))
+ "https://github.com/vcftools/vcftools/releases/download/v"
+ version "/vcftools-" version ".tar.gz"))
(sha256
(base32
- "148al9h7f8g8my2qdnpax51kdd2yjrivlx6frvakf4lz5r8j88wx"))))
+ "10l5c07z9p4i9pr4gl54b2c9h6ndhqlbq1rashg2zcgwkbfrkmvn"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no "check" target
@@ -3707,18 +3708,13 @@ Cuffdiff or Ballgown programs.")
"CFLAGS=-O2" ; override "-m64" flag
(string-append "PREFIX=" (assoc-ref %outputs "out"))
(string-append "MANDIR=" (assoc-ref %outputs "out")
- "/share/man/man1"))
- #:phases
- (alist-cons-after
- 'unpack 'patch-manpage-install
- (lambda _
- (substitute* "Makefile"
- (("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1")))
- (alist-delete 'configure %standard-phases))))
+ "/share/man/man1"))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
(inputs
`(("perl" ,perl)
("zlib" ,zlib)))
- (home-page "http://vcftools.sourceforge.net/")
+ (home-page "https://vcftools.github.io/")
(synopsis "Tools for working with VCF files")
(description
"VCFtools is a program package designed for working with VCF files, such
@@ -3726,7 +3722,7 @@ as those generated by the 1000 Genomes Project. The aim of VCFtools is to
provide easily accessible methods for working with complex genetic variation
data in the form of VCF files.")
;; The license is declared as LGPLv3 in the README and
- ;; at http://vcftools.sourceforge.net/license.html
+ ;; at https://vcftools.github.io/license.html
(license license:lgpl3)))
(define-public vsearch
@@ -3927,8 +3923,7 @@ barplots or heatmaps.")
(base32
"0f16ryy5f012hvksrwlmm33bcl7lw97i2jvhbnwfwl03j4w7nhc1"))))
(properties
- `((upstream-name . "BiocGenerics")
- (r-repository . bioconductor)))
+ `((upstream-name . "BiocGenerics")))
(build-system r-build-system)
(home-page "http://bioconductor.org/packages/BiocGenerics")
(synopsis "S4 generic functions for Bioconductor")
@@ -3970,8 +3965,7 @@ abnormal copy number.")
(base32
"12iibcs63m9iy7f45wgjcqsna2dnqwckphk682389grshz0g4x66"))))
(properties
- `((upstream-name . "S4Vectors")
- (r-repository . bioconductor)))
+ `((upstream-name . "S4Vectors")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)))
@@ -3998,8 +3992,7 @@ S4Vectors package itself.")
(base32
"0hi5k1j5jm4xrg1l506g279qw1xkvp1gg1zgsjzpbng4vx4k4iyl"))))
(properties
- `((upstream-name . "IRanges")
- (r-repository . bioconductor)))
+ `((upstream-name . "IRanges")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
@@ -4020,16 +4013,15 @@ possible.")
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.6.1")
+ (version "1.6.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "1j2n1v1mrw1fxn7cyffz112pm76wd6gy9q9qwlsfv3brbsqbvdbf"))))
+ "1ggp005n2rlkad00ilzn95y4rd484yr1chdhnd6fwg45rbi94d63"))))
(properties
- `((upstream-name . "GenomeInfoDb")
- (r-repository . bioconductor)))
+ `((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
@@ -4055,8 +4047,7 @@ names in their natural, rather than lexicographic, order.")
(base32
"0havwyr6xqk7w0rmbwfj9jq1djz7wzdz7w39adhklwzwz9l4ih3a"))))
(properties
- `((upstream-name . "XVector")
- (r-repository . bioconductor)))
+ `((upstream-name . "XVector")))
(build-system r-build-system)
(arguments
`(#:phases
@@ -4084,16 +4075,15 @@ names in their natural, rather than lexicographic, order.")
(define-public r-genomicranges
(package
(name "r-genomicranges")
- (version "1.22.2")
+ (version "1.22.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicRanges" version))
(sha256
(base32
- "1jffvcs0jsi7q4l3pvjj6r73vll80csgkljvhqp0g2ixc43jjng9"))))
+ "02df5683nrpn9d10ws8jz9b55nr9055hh882xp2i154xdddir0k0"))))
(properties
- `((upstream-name . "GenomicRanges")
- (r-repository . bioconductor)))
+ `((upstream-name . "GenomicRanges")))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
@@ -4215,13 +4205,13 @@ objects.")
(define-public r-biostrings
(package
(name "r-biostrings")
- (version "2.38.2")
+ (version "2.38.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biostrings" version))
(sha256
(base32
- "1afp9szc8ci6jn0m3hrrqh6df65cpw3v1dcnl6xir3d3m3lwwmk4"))))
+ "0cjd7i4bdwabzb02gm753aji5xaihkj5ak8nb0d32cclxbj0hp33"))))
(properties
`((upstream-name . "Biostrings")))
(build-system r-build-system)
@@ -4285,13 +4275,13 @@ files.")
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
- (version "1.0.1")
+ (version "1.0.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
- "0w1dwp99p6i7sc3cn0ir3dr8ksgxwjf16675h5i8n6gbv4rl9lz6"))))
+ "1gpmh1mi70m5k5qnyjs1h0qn8ajrzalzic7k3762xchxsmmdvxn4"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
@@ -4314,13 +4304,13 @@ samples.")
(define-public r-genomicalignments
(package
(name "r-genomicalignments")
- (version "1.6.1")
+ (version "1.6.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicAlignments" version))
(sha256
(base32
- "03pxzkmwcpl0d7a09ahan0nllfv7qw2i7w361w6af2s4n3xwrniz"))))
+ "02b9j1pfd39bkvb623k5k0ziq9rpw093hifqw65vb954dwj29jhd"))))
(properties
`((upstream-name . "GenomicAlignments")))
(build-system r-build-system)
@@ -4347,13 +4337,13 @@ alignments.")
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.30.1")
+ (version "1.30.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "1if31hg56islx5vwydpgs5gkyas26kyvv2ljv1c7jikpm62w14qv"))))
+ "0knjnwywh9k726mq28s3sy013zhw6d6nfa8hfw670720nq18i2p0"))))
(build-system r-build-system)
(arguments
`(#:phases
@@ -4392,13 +4382,13 @@ as well as query and modify the browser state, such as the current viewport.")
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.22.7")
+ (version "1.22.13")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "1jb4s49ar5j9qslpd3kfdg2wrl4q7ciysd55h9a7zvspymxcngq8"))))
+ "0n3rkj66la6wizgcsf2rmwcsyfxz9kv5zak337lmk1raqfnancz4"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
@@ -4582,13 +4572,13 @@ reference point and sorted by a user defined feature.")
(define-public r-genomation
(package
(name "r-genomation")
- (version "1.2.1")
+ (version "1.2.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "genomation" version))
(sha256
(base32
- "1mzs995snwim13qk9kz4q3nczpnbsy1allwp4whfq0cflg2mndfr"))))
+ "0kvzwc21zsh2c8d34yn935ncn38bfkpzmknycd8h7b0521x20mi9"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biostrings" ,r-biostrings)
generated by cgit v1.2.3 (git 2.45.0) at 2024-12-19 01:44:33 +0000