;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (srfi srfi-1)
#:use-module (ice-9 match))
-(define-public r-ape
- (package
- (name "r-ape")
- (version "5.0")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "ape" version))
- (sha256
- (base32
- "0q59pmxawz498cb9mv5m49lhiwxib8ak94yyydz7qg8b6lpd4bn3"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-lattice" ,r-lattice)
- ("r-nlme" ,r-nlme)
- ("r-rcpp" ,r-rcpp)))
- (home-page "http://ape-package.ird.fr/")
- (synopsis "Analyses of phylogenetics and evolution")
- (description
- "This package provides functions for reading, writing, plotting, and
-manipulating phylogenetic trees, analyses of comparative data in a
-phylogenetic framework, ancestral character analyses, analyses of
-diversification and macroevolution, computing distances from DNA sequences,
-and several other tools.")
- (license license:gpl2+)))
-
(define-public aragorn
(package
(name "aragorn")
(define-public bamtools
(package
(name "bamtools")
- (version "2.4.1")
+ (version "2.5.1")
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0jr024kcrhjb82cm69i7p5fcg5375zlc1h3qh2n1v368hcd0qflk"))))
+ "1z3kg24qrwq13a88n9d86izngrar4fll7gr6phddb2faw75pdgaa"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ;no "check" target
(define-public bcftools
(package
(name "bcftools")
- (version "1.5")
+ (version "1.8")
(source (origin
(method url-fetch)
(uri (string-append
version "/bcftools-" version ".tar.bz2"))
(sha256
(base32
- "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"))
- (patches (search-patches "bcftools-regidx-unsigned-char.patch"))
+ "1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa"))
(modules '((guix build utils)))
(snippet
;; Delete bundled htslib.
- '(delete-file-recursively "htslib-1.5"))))
+ '(delete-file-recursively "htslib-1.8"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
(define-public bedops
(package
(name "bedops")
- (version "2.4.14")
+ (version "2.4.33")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/bedops/bedops/archive/v"
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v"))))
+ "0kx4awrwby8f33wqyx8w7ms7v25xhf0d421csgf96a3hfzn2mb0m"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f
identify enrichments with functional annotations of the genome.")
(license license:gpl3+)))
+(define-public delly
+ (package
+ (name "delly")
+ (version "0.7.7")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/tobiasrausch/delly/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj"))
+ (patches (search-patches "delly-use-system-libraries.patch"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'install
+ (lambda _
+ (let ((bin (string-append (assoc-ref %outputs "out") "/bin"))
+ (templates (string-append (assoc-ref %outputs "out")
+ "/share/delly/templates")))
+ (mkdir-p bin)
+ (mkdir-p templates)
+ (copy-recursively "excludeTemplates" templates)
+ (install-file "src/cov" bin)
+ (install-file "src/delly" bin)
+ (install-file "src/dpe" bin)))))))
+ (native-inputs
+ `(("python" ,python-2)))
+ (inputs
+ `(("boost" ,boost)
+ ("htslib" ,htslib)
+ ("zlib" ,zlib)
+ ("bzip2" ,bzip2)))
+ (home-page "https://github.com/tobiasrausch/delly")
+ (synopsis "Integrated structural variant prediction method")
+ (description "Delly is an integrated structural variant prediction method
+that can discover and genotype deletions, tandem duplications, inversions and
+translocations at single-nucleotide resolution in short-read massively parallel
+sequencing data. It uses paired-ends and split-reads to sensitively and
+accurately delineate genomic rearrangements throughout the genome.")
+ (license license:gpl3+)))
+
(define-public diamond
(package
(name "diamond")
- (version "0.9.18")
+ (version "0.9.22")
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1vi2nddmy7knrv8gsprwqp6a40k63n3f2dfvx22ipjhrg9xir96f"))))
+ "0adp87r9ak63frdrdmrdfhsn6g0jnnyq1lr2wibvqbxcl37iir9m"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no "check" target
(string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
(substitute* "src/CMakeLists.txt"
(("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
- (string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
+ (string-append (assoc-ref inputs "bamtools") "/lib"))
+ (("libprotobuf.a") "libprotobuf.so"))
#t)))))
(inputs
`(("boost" ,boost)
@end itemize\n")
(license license:gpl3+)))
+(define-public fastp
+ (package
+ (name "fastp")
+ (version "0.14.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/OpenGene/fastp.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1r6ms5zbf5rps4rgp4z73nczadl00b5rqylw8f684isfz27dp0xh"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are none
+ #:make-flags
+ (list (string-append "BINDIR=" (assoc-ref %outputs "out") "/bin"))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'install 'create-target-dir
+ (lambda* (#:key outputs #:allow-other-keys)
+ (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
+ #t)))))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://github.com/OpenGene/fastp/")
+ (synopsis "All-in-one FastQ preprocessor")
+ (description
+ "Fastp is a tool designed to provide fast all-in-one preprocessing for
+FastQ files. This tool has multi-threading support to afford high
+performance.")
+ (license license:expat)))
+
(define-public htslib
(package
(name "htslib")
- (version "1.7")
+ (version "1.8")
(source (origin
(method url-fetch)
(uri (string-append
version "/htslib-" version ".tar.bz2"))
(sha256
(base32
- "1il6i2p84b0y9c93dhvzzki1ifw9bvapm2mvpr0xvb2nq8jlwgdy"))))
+ "18bw0mn9pj5wgarnlaxmf1bb8pdqgl1zd6czirqcr62ajpn1xvy0"))))
(build-system gnu-build-system)
(inputs
`(("openssl" ,openssl)
(define-public kaiju
(package
(name "kaiju")
- (version "1.5.0")
+ (version "1.6.2")
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0afbfalfw9y39bkwnqjrh9bghs118ws1pzj5h8l0nblgn3mbjdks"))))
+ "1kdn4rxs0kr9ibmrgrfcci71aa6j6gr71dbc8pff7731rpab6kj7"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; There are no tests.
(copy-recursively "util" bin))
#t)))))
(inputs
- `(("perl" ,perl)))
+ `(("perl" ,perl)
+ ("zlib" ,zlib)))
(home-page "http://kaiju.binf.ku.dk/")
(synopsis "Fast and sensitive taxonomic classification for metagenomics")
(description "Kaiju is a program for sensitive taxonomic classification
(define-public mafft
(package
(name "mafft")
- (version "7.313")
+ (version "7.394")
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tgz"))
(sha256
(base32
- "0r83qmg2if8mi6jyx3xdf8ar2gcxl7r9nmj98jr7lxym97v61a2k"))))
+ "0bacjkxfg944p5khhyh5rd4y7wkjc9qk4v2jjj442sqlq0f8ar7b"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no automated tests, though there are tests in the read me
(define-public mash
(package
(name "mash")
- (version "1.1.1")
+ (version "2.0")
(source (origin
(method url-fetch)
(uri (string-append
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "08znbvqq5xknfhmpp3wcj574zvi4p7i8zifi67c9qw9a6ikp42fj"))
+ "00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv"))
(modules '((guix build utils)))
(snippet
;; Delete bundled kseq.
(modify-phases %standard-phases
(add-after 'unpack 'fix-includes
(lambda _
- (substitute* '("src/mash/Sketch.cpp" "src/mash/CommandFind.cpp")
+ (substitute* '("src/mash/Sketch.cpp"
+ "src/mash/CommandFind.cpp"
+ "src/mash/CommandScreen.cpp")
(("^#include \"kseq\\.h\"")
"#include \"htslib/kseq.h\""))
#t))
(define-public roary
(package
(name "roary")
- (version "3.11.0")
+ (version "3.12.0")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "10lw78x1xzvn7xzvnmh4bm3cak3ah5cssapl0yidvhaj1f44h29i"))))
+ "0qxrds9wx7cfhlkihrp6697kx0flhhxymap9fwan0b3rbdhcnmff"))))
(build-system perl-build-system)
(arguments
`(#:phases
(define-public samtools
(package
(name "samtools")
- (version "1.7")
+ (version "1.8")
(source
(origin
(method url-fetch)
version "/samtools-" version ".tar.bz2"))
(sha256
(base32
- "18acyqysbxpydlc44lqv2hpp57l06bs9a3yqmcvjk8va2xrrdc77"))))
+ "05myg7bs90i68qbqab9cdg9rqj2xh39azibrx82ipzc5kcfvqhn9"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((ice-9 ftw)
(define-public star
(package
(name "star")
- (version "2.5.3a")
+ (version "2.6.0a")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/alexdobin/STAR/archive/"
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "013wirlz8lllgjyagl48l75n1isxyabqb3sj7qlsl0x1rmvqw99a"))
+ "0yci4ymy4407kjh0lqp021nzccp6r31wgrkixkmix5p130cxvc56"))
(modules '((guix build utils)))
(snippet
'(begin
(define-public taxtastic
(package
(name "taxtastic")
- (version "0.6.4")
+ (version "0.8.5")
(source (origin
(method url-fetch)
(uri (pypi-uri "taxtastic" version))
(sha256
(base32
- "0s79z8kfl853x7l4h8ms05k31q87aw62nrchlk20w9n227j35929"))))
+ "03pysw79lsrvz4lwzis88j15067ffqbi4cid5pqhrlxmd6bh8rrk"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
(define-public r-vegan
(package
(name "r-vegan")
- (version "2.4-6")
+ (version "2.5-2")
(source
(origin
(method url-fetch)
(uri (cran-uri "vegan" version))
(sha256
(base32
- "175mqr42mmxy98gpf3rky8alnkw3w1k90ggdw3cispl36841p76w"))))
+ "13pyqvlpz64qibi8k5d109v7q09j06mbv6ndix3n4cn21mjx391c"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(propagated-inputs
`(("r-cluster" ,r-cluster)
+ ("r-knitr" ,r-knitr) ; needed for vignettes
("r-lattice" ,r-lattice)
("r-mass" ,r-mass)
("r-mgcv" ,r-mgcv)
(define-public r-annotate
(package
(name "r-annotate")
- (version "1.56.1")
+ (version "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotate" version))
(sha256
(base32
- "14c5xd9kasvcwg5gbjys2c1vizxhlqlzxakqc2kml0kw97hmx0rq"))))
+ "1qmncyvy147a1ll3iri45p822kcs3s7583jfnq9jf6sz9ilk8cjf"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
(define-public r-copynumber
(package
(name "r-copynumber")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "copynumber" version))
(sha256
(base32
- "01kcwzl485yjrkgyg8117b1il957ss0v6rq4bbxf4ksd5fzcjmyx"))))
+ "0y9nnwb0psphp3ix88wj2f8z5gr45r5znf55w892ysm27isdpmms"))))
(build-system r-build-system)
(propagated-inputs
`(("r-s4vectors" ,r-s4vectors)
(define-public r-geneplotter
(package
(name "r-geneplotter")
- (version "1.56.0")
+ (version "1.58.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "geneplotter" version))
(sha256
(base32
- "1z3g7frc1iviwrsv2dlm4nqvkc0685h4va0388yfxn102ln8wwma"))))
+ "055g28xgiazl4l0gkg8xiamks64f5yckjjyvw1abd6d6qjavwx0g"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotate" ,r-annotate)
(define-public r-genefilter
(package
(name "r-genefilter")
- (version "1.60.0")
+ (version "1.62.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "genefilter" version))
(sha256
(base32
- "173swlg6gj4kdllbqvyiw5dggbcxiwlwpqmllsv4dxzn7h25i3g7"))))
+ "14l0ff02spmjwxj0m1czhg5vlkgwcfi73cym8m2n9vn6i7bjdaqi"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(define-public r-dexseq
(package
(name "r-dexseq")
- (version "1.24.3")
+ (version "1.24.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DEXSeq" version))
(sha256
(base32
- "0xip73hlbr3zry9d7ly9vvvsbb3xjcmfa09lr9fdy528dwjrf084"))))
+ "1a80yv742fx5c7qav7imsdybphf0d5bixsqyf8w5zng7fk8j16d5"))))
(properties `((upstream-name . "DEXSeq")))
(build-system r-build-system)
(propagated-inputs
(define-public vsearch
(package
(name "vsearch")
- (version "2.7.1")
+ (version "2.8.0")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0jlzfgh79fzmb4g7sngzdjjsjyc37icvs1k7vmc2ksxglj6x5i7f"))
+ "15pbirgzhvflj4pi5n82vybbzjy9mlb0lv5l3qhrmdkfzpbyahw3"))
(patches (search-patches "vsearch-unbundle-cityhash.patch"))
(snippet
'(begin
("r-rmarkdown" ,r-rmarkdown)
("r-tinytex" ,r-tinytex)
("r-yaml" ,r-yaml)
- ("r-xfun" ,r-xfun)
- ("ghc-pandoc" ,ghc-pandoc)))
+ ("r-xfun" ,r-xfun)))
(home-page "https://github.com/rstudio/bookdown")
(synopsis "Authoring books and technical documents with R markdown")
(description "This package provides output formats and utilities for
(define-public r-genomicalignments
(package
(name "r-genomicalignments")
- (version "1.14.1")
+ (version "1.14.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicAlignments" version))
(sha256
(base32
- "033p6fw46sn7w2yyn14nb9qcnkf30cl0nv6zh014ixflm3iifz39"))))
+ "1659nj1xps7vliy5955i51x6hvrf16n1z0dfh10mmpaaswn2d2mv"))))
(properties
`((upstream-name . "GenomicAlignments")))
(build-system r-build-system)
("r-testthat" ,r-testthat)
;; During vignette building knitr checks that "pandoc-citeproc"
;; is in the PATH.
- ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)))
+ ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)))
(propagated-inputs
`(("r-data-table" ,r-data-table)
("r-biomart" ,r-biomart)
(define-public r-mutationalpatterns
(package
(name "r-mutationalpatterns")
- (version "1.4.2")
+ (version "1.4.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MutationalPatterns" version))
(sha256
(base32
- "08ay9h5cqsi8ypb6r0g4rfa5l1g06jgfzl64wmhgz134yqbl7vfv"))))
+ "0ml4gsp5dfv23xqrknxh25q8q65hly1xb1215lcwyc8hj9z8f941"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-genomicranges" ,r-genomicranges)
("r-genomeinfodb" ,r-genomeinfodb)
("r-ggplot2" ,r-ggplot2)
- ("r-gridextra" ,r-gridextra)
("r-iranges" ,r-iranges)
("r-nmf" ,r-nmf)
("r-plyr" ,r-plyr)
(define-public multiqc
(package
(name "multiqc")
- (version "1.4")
+ (version "1.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "multiqc" version))
(sha256
(base32
- "0ihx4rzmsfphv4byn05qv6f1y95g2dxs6viwziipl4wjk96acgm8"))))
+ "02iihfl0w0hpnr4pa0sbd1y9qxrg3ycyhjp5lidkcrqh1lmzs3zy"))))
(build-system python-build-system)
(propagated-inputs
`(("python-jinja2" ,python-jinja2)
("python-numpy" ,python-numpy)
;; MultQC checks for the presence of nose at runtime.
("python-nose" ,python-nose)))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "setup.py"
+ ;; MultiQC 1.5 ‘requires’ a version of python-matplotlib older
+ ;; than the one in Guix, but should work fine with 2.2.2.
+ ;; See <https://github.com/ewels/MultiQC/issues/725> and
+ ;; <https://github.com/ewels/MultiQC/issues/732> for details.
+ (("['\"]matplotlib.*?['\"]")
+ "'matplotlib'"))
+ #t)))))
(home-page "http://multiqc.info")
(synopsis "Aggregate bioinformatics analysis reports")
(description
(define-public r-seurat
(package
(name "r-seurat")
- (version "2.2.1")
+ (version "2.3.1")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
- "1sr82nf38hq07avrfn8vlrzjq7dfm4pcr8l1nh6mnglcql2bk9z2"))
+ "0hi59rgdrr2iqfvx5bq7yq02hbjxkjl1fzidqj14z0ypq0nzbjys"))
;; Delete pre-built jar.
(snippet
'(begin (delete-file "inst/java/ModularityOptimizer.jar")
(propagated-inputs
`(("r-ape" ,r-ape)
("r-caret" ,r-caret)
+ ("r-cluster" ,r-cluster)
("r-cowplot" ,r-cowplot)
("r-diffusionmap" ,r-diffusionmap)
+ ("r-dosnow" ,r-dosnow)
("r-dplyr" ,r-dplyr)
("r-dtw" ,r-dtw)
+ ("r-fitdistrplus" ,r-fitdistrplus)
("r-fnn" ,r-fnn)
+ ("r-foreach" ,r-foreach)
("r-fpc" ,r-fpc)
("r-gdata" ,r-gdata)
("r-ggplot2" ,r-ggplot2)
("r-ggridges" ,r-ggridges)
("r-gplots" ,r-gplots)
- ("r-gridextra" ,r-gridextra)
("r-hmisc" ,r-hmisc)
("r-ica" ,r-ica)
("r-igraph" ,r-igraph)
("r-irlba" ,r-irlba)
("r-lars" ,r-lars)
+ ("r-lmtest" ,r-lmtest)
("r-mass" ,r-mass)
("r-matrix" ,r-matrix)
("r-metap" ,r-metap)
("r-mixtools" ,r-mixtools)
("r-pbapply" ,r-pbapply)
("r-plotly" ,r-plotly)
+ ("r-png" ,r-png)
("r-ranger" ,r-ranger)
+ ("r-rann" ,r-rann)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-rcpp" ,r-rcpp)
("r-rcppeigen" ,r-rcppeigen)
("r-rcppprogress" ,r-rcppprogress)
("r-reshape2" ,r-reshape2)
+ ("r-reticulate" ,r-reticulate)
("r-rocr" ,r-rocr)
("r-rtsne" ,r-rtsne)
("r-sdmtools" ,r-sdmtools)
(define-public r-ggbio
(package
(name "r-ggbio")
- (version "1.26.0")
+ (version "1.26.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggbio" version))
(sha256
(base32
- "1bqxfqy0hff87ax92z4lfbjz01ndrz7x8pzm6dlkdmi52p30krm9"))))
+ "1xlmlngn27iwnr21s9di4059kav1a7c1sajx08wja8yn8f7j06hp"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
(define-public r-gprofiler
(package
(name "r-gprofiler")
- (version "0.6.4")
+ (version "0.6.6")
(source
(origin
(method url-fetch)
(uri (cran-uri "gProfileR" version))
(sha256
(base32
- "1cka02zbz1rbppm782qpxk1xn9qxbrv2gp5rgf970j906hxm2y0b"))))
+ "1n6cj12j102b4x9vhyl4dljp1i0r43p23cnhqbx4als2xfxdlqgi"))))
(properties `((upstream-name . "gProfileR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-erma
(package
(name "r-erma")
- (version "0.10.0")
+ (version "0.10.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "erma" version))
(sha256
(base32
- "0gcfs9g8vvdv5vmq9b21kd8sq5mizjj49nfzd4in9zvp4b9v7x1g"))))
+ "1fi8nc6fbd7i4p9i9hli31xplmdpsxqcdrb8v3nf8fx9klllbdav"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
(define-public r-ldblock
(package
(name "r-ldblock")
- (version "1.8.0")
+ (version "1.8.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ldblock" version))
(sha256
(base32
- "18nfsixh6d2wfrb9laqsgly5w1frzihhak683k0p8fdf51h4aqba"))))
+ "1q8dz8wcq1r7kr635s9q21g36sxkdybk8khhpa4p57qv8r0gppl0"))))
(build-system r-build-system)
(propagated-inputs
`(("r-erma" ,r-erma)
(define-public r-hitc
(package
(name "r-hitc")
- (version "1.22.0")
+ (version "1.22.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "HiTC" version))
(sha256
(base32
- "0288xa1jy6nzvz2ha07csmp6dirjw5r7p9vy69q2wsbyzr02ymkp"))))
+ "0da1jw9my2n2gihs31zyn14wwr23d8v2vij39ll7rm6fma3ydfbl"))))
(properties `((upstream-name . "HiTC")))
(build-system r-build-system)
(propagated-inputs
(invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
(rename-file (string-append "hdf5-" ,(package-version hdf5))
"hdf5")
+ ;; Remove timestamp and host system information to make
+ ;; the build reproducible.
+ (substitute* "hdf5/src/libhdf5.settings.in"
+ (("Configured on: @CONFIG_DATE@")
+ "Configured on: Guix")
+ (("Uname information:.*")
+ "Uname information: Linux\n")
+ ;; Remove unnecessary store reference.
+ (("C Compiler:.*")
+ "C Compiler: GCC\n"))
(rename-file "Makevars.in" "Makevars")
(substitute* "Makevars"
(("HDF5_CXX_LIB=.*")
(define-public r-scran
(package
(name "r-scran")
- (version "1.6.8")
+ (version "1.6.9")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scran" version))
(sha256
(base32
- "07wniyrh2fhhkz28v0bfgpvpi1hkkn2cvhacrvvvck142j79944x"))))
+ "0cs64cnf0xjcgmawr210y99j3gxs6aqgh8081n9827kkqnx2y5dm"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
memory usage and processing time is minimized.")
(license license:expat)))
+(define-public r-phangorn
+ (package
+ (name "r-phangorn")
+ (version "2.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "phangorn" version))
+ (sha256
+ (base32
+ "0xc8k552nxczy19jr0xjjagrzc8x6lafasgk2c099ls8bc1yml1i"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-fastmatch" ,r-fastmatch)
+ ("r-igraph" ,r-igraph)
+ ("r-magrittr" ,r-magrittr)
+ ("r-matrix" ,r-matrix)
+ ("r-quadprog" ,r-quadprog)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/KlausVigo/phangorn")
+ (synopsis "Phylogenetic analysis in R")
+ (description
+ "Phangorn is a package for phylogenetic analysis in R. It supports
+estimation of phylogenetic trees and networks using Maximum Likelihood,
+Maximum Parsimony, distance methods and Hadamard conjugation.")
+ (license license:gpl2+)))
+
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
(base32
"0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9"))))
(arguments
- (substitute-keyword-arguments (package-arguments htslib)
- ((#:phases phases)
- `(modify-phases ,phases
- (add-after 'unpack 'bootstrap
- (lambda _
- (zero? (system* "autoreconf" "-vif"))))))))
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'bootstrap
+ (lambda _ (invoke "autoreconf" "-vif"))))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
(define-public sambamba
(package
(name "sambamba")
- (version "0.6.5")
+ (version "0.6.7-10-g223fa20")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/lomereiter/sambamba/"
- "archive/v" version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/lomereiter/sambamba.git")
+ (commit (string-append "v" version))))
+ (file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "17076gijd65a3f07zns2gvbgahiz5lriwsa6dq353ss3jl85d8vy"))))
+ "1zb9hrxglxqh13ava9wwri30cvf85hjnbn8ccnr8l60a3k5avczn"))))
(build-system gnu-build-system)
(arguments
- `(#:tests? #f ; there is no test target
- #:make-flags
- '("D_COMPILER=ldc2"
- ;; Override "--compiler" flag only.
- "D_FLAGS=--compiler=ldc2 -IBioD -g -d"
- "sambamba-ldmd2-64")
+ `(#:tests? #f ; there is no test target
+ #:parallel-build? #f ; not supported
#:phases
(modify-phases %standard-phases
(delete 'configure)
- (add-after 'unpack 'place-biod
+ (add-after 'unpack 'fix-ldc-version
+ (lambda _
+ (substitute* "gen_ldc_version_info.py"
+ (("/usr/bin/env.*") (which "python")))
+ (substitute* "Makefile"
+ (("\\$\\(shell which ldmd2\\)") (which "ldmd2")))
+ #t))
+ (add-after 'unpack 'place-biod-and-undead
(lambda* (#:key inputs #:allow-other-keys)
(copy-recursively (assoc-ref inputs "biod") "BioD")
+ (copy-recursively (assoc-ref inputs "undead") "undeaD")
#t))
(add-after 'unpack 'unbundle-prerequisites
(lambda _
(substitute* "Makefile"
+ (("htslib/libhts.a lz4/lib/liblz4.a")
+ "-L-lhts -L-llz4")
((" htslib-static lz4-static") ""))
#t))
(replace 'install
(native-inputs
`(("ldc" ,ldc)
("rdmd" ,rdmd)
+ ("python" ,python2-minimal)
("biod"
- ,(let ((commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587"))
+ ,(let ((commit "c778e4f2d8bacea7499283ce39f5577b232732c6"))
(origin
(method git-fetch)
(uri (git-reference
"-checkout"))
(sha256
(base32
- "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3")))))))
+ "1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37")))))
+ ("undead"
+ ,(let ((commit "92803d25c88657e945511f0976a0c79d8da46e89"))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dlang/undeaD.git")
+ (commit commit)))
+ (file-name (string-append "undead-"
+ (string-take commit 9)
+ "-checkout"))
+ (sha256
+ (base32
+ "0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138")))))))
(inputs
`(("lz4" ,lz4)
("htslib" ,htslib-for-sambamba)))
(define-public trim-galore
(package
(name "trim-galore")
- (version "0.4.2")
+ (version "0.4.5")
(source
(origin
- (method url-fetch)
- (uri (string-append "http://www.bioinformatics.babraham.ac.uk/"
- "projects/trim_galore/trim_galore_v"
- version ".zip"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/FelixKrueger/TrimGalore.git")
+ (commit version)))
+ (file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "0b9qdxi4521gsrjvbhgky8g7kry9b5nx3byzaxkgxz7p4k8bn1mn"))))
+ "0x5892l48c816pf00wmnz5vq0zq6170d3xc8zrxncd4jcz7h1p71"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no tests
#:phases
(modify-phases %standard-phases
- ;; The archive contains plain files.
- (replace 'unpack
- (lambda* (#:key source #:allow-other-keys)
- (zero? (system* "unzip" source))))
(delete 'configure)
(delete 'build)
(add-after 'unpack 'hardcode-tool-references
("tcsh" ,tcsh)
("perl" ,perl)
("libpng" ,libpng)
- ("mysql" ,mysql)
+ ("mariadb" ,mariadb)
("openssl" ,openssl)))
(home-page "http://genome.cse.ucsc.edu/index.html")
(synopsis "Assorted bioinformatics utilities")
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((target (assoc-ref outputs "out"))
- (doc (string-append target "/share/doc/f-seq/")))
+ (bin (string-append target "/bin"))
+ (doc (string-append target "/share/doc/f-seq"))
+ (lib (string-append target "/lib")))
(mkdir-p target)
(mkdir-p doc)
(substitute* "bin/linux/fseq"
(string-append (assoc-ref inputs "java-commons-cli")
"/share/java/commons-cli.jar"))
(("REALDIR=.*")
- (string-append "REALDIR=" target "/bin\n")))
+ (string-append "REALDIR=" bin "\n")))
(install-file "README.txt" doc)
- (install-file "bin/linux/fseq" (string-append target "/bin"))
- (install-file "build~/fseq.jar" (string-append target "/lib"))
- (copy-recursively "lib" (string-append target "/lib"))
+ (install-file "bin/linux/fseq" bin)
+ (install-file "build~/fseq.jar" lib)
+ (copy-recursively "lib" lib)
#t))))))
(inputs
`(("perl" ,perl)
(define-public bismark
(package
(name "bismark")
- (version "0.16.3")
+ (version "0.19.1")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/FelixKrueger/Bismark/"
- "archive/" version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/FelixKrueger/Bismark.git")
+ (commit version)))
+ (file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "1204i0pa02ll2jn5pnxypkclnskvv7a2nwh5nxhagmhxk9wfv9sq"))))
+ "0yb5l36slwg02fp4b1jdlplgljcsxgqfzvzihzdnphd87dghcc84"))
+ (snippet
+ '(begin
+ ;; highcharts.js is non-free software. The code is available under
+ ;; CC-BY-NC or proprietary licenses only.
+ (delete-file "bismark_sitrep/highcharts.js")
+ #t))))
(build-system perl-build-system)
(arguments
- `(#:tests? #f ; there are no tests
+ `(#:tests? #f ; there are no tests
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out")
- "/bin"))
- (docdir (string-append (assoc-ref outputs "out")
- "/share/doc/bismark"))
- (docs '("Bismark_User_Guide.pdf"
- "RELEASE_NOTES.txt"))
- (scripts '("bismark"
- "bismark_genome_preparation"
- "bismark_methylation_extractor"
- "bismark2bedGraph"
- "bismark2report"
- "coverage2cytosine"
- "deduplicate_bismark"
- "bismark_sitrep.tpl"
- "bam2nuc"
- "bismark2summary")))
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (share (string-append out "/share/bismark"))
+ (docdir (string-append out "/share/doc/bismark"))
+ (docs '("Docs/Bismark_User_Guide.html"))
+ (scripts '("bismark"
+ "bismark_genome_preparation"
+ "bismark_methylation_extractor"
+ "bismark2bedGraph"
+ "bismark2report"
+ "coverage2cytosine"
+ "deduplicate_bismark"
+ "filter_non_conversion"
+ "bam2nuc"
+ "bismark2summary")))
+ (substitute* "bismark2report"
+ (("\\$RealBin/bismark_sitrep")
+ (string-append share "/bismark_sitrep")))
+ (mkdir-p share)
(mkdir-p docdir)
(mkdir-p bin)
(for-each (lambda (file) (install-file file bin))
scripts)
(for-each (lambda (file) (install-file file docdir))
docs)
+ (copy-recursively "Docs/Images" (string-append docdir "/Images"))
+ (copy-recursively "bismark_sitrep"
+ (string-append share "/bismark_sitrep"))
+
+ ;; Fix references to gunzip
+ (substitute* (map (lambda (file)
+ (string-append bin "/" file))
+ scripts)
+ (("\"gunzip -c")
+ (string-append "\"" (assoc-ref inputs "gzip")
+ "/bin/gunzip -c")))
#t))))))
+ (inputs
+ `(("gzip" ,gzip)))
(home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/")
(synopsis "Map bisulfite treated sequence reads and analyze methylation")
(description "Bismark is a program to map bisulfite treated sequencing
code that is used in the Cufflinks codebase. The goal of this library is to
provide this functionality without the necessity of drawing in a heavy-weight
dependency like SeqAn.")
- (license (license:x11-style "http://www.boost.org/LICENSE_1_0.txt"))))
+ (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt"))))
(define-public libdivsufsort
(package
(define-public pigx-rnaseq
(package
(name "pigx-rnaseq")
- (version "0.0.2")
+ (version "0.0.3")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
"/pigx_rnaseq-" version ".tar.gz"))
(sha256
(base32
- "168hx2ig3rarphx3l21ay9yyg8ipaakzixnrhpbdi0sknhyvrrk8"))))
+ "0pz080k4ajlc4rlznkn3najy2a6874gb56rf9g4ag9wqz31q174j"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-tests? #f ; not supported
#:phases
(modify-phases %standard-phases
+ ;; "test.sh" runs STAR, which requires excessive amounts of memory.
+ (add-after 'unpack 'disable-resource-intensive-test
+ (lambda _
+ (substitute* "Makefile.in"
+ (("(^ tests/test_trim_galore/test.sh).*" _ m) m)
+ (("^ test.sh") ""))
+ #t))
(add-after 'install 'wrap-executable
;; Make sure the executable finds all R modules.
(lambda* (#:key inputs outputs #:allow-other-keys)
`("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
#t)))))
(inputs
- `(("snakemake" ,snakemake)
+ `(("gzip" ,gzip)
+ ("snakemake" ,snakemake)
("fastqc" ,fastqc)
("multiqc" ,multiqc)
("star" ,star)
("r-rtracklayer" ,r-rtracklayer)
("r-rjson" ,r-rjson)
("salmon" ,salmon)
- ("ghc-pandoc" ,ghc-pandoc)
- ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
+ ("ghc-pandoc" ,ghc-pandoc-1)
+ ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
("python-wrapper" ,python-wrapper)
("python-pyyaml" ,python-pyyaml)))
(home-page "http://bioinformatics.mdc-berlin.de/pigx/")
quality control of the experiment, the pipeline produces a differential
expression report comparing samples in an easily configurable manner.")
(license license:gpl3+)))
+
+(define-public pigx-chipseq
+ (package
+ (name "pigx-chipseq")
+ (version "0.0.15")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
+ "releases/download/v" version
+ "/pigx_chipseq-" version ".tar.gz"))
+ (sha256
+ (base32
+ "11v9v3vyda0sv4cl45nki7mm4v4bjfcdq7a70kcvi9h465nq66wg"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; parts of the tests rely on access to the network
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'install 'wrap-executable
+ ;; Make sure the executable finds all R modules.
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (wrap-program (string-append out "/bin/pigx-chipseq")
+ `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
+ `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
+ #t)))))
+ (inputs
+ `(("grep" ,grep)
+ ("coreutils" ,coreutils)
+ ("r-minimal" ,r-minimal)
+ ("r-argparser" ,r-argparser)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-chipseq" ,r-chipseq)
+ ("r-data-table" ,r-data-table)
+ ("r-dplyr" ,r-dplyr)
+ ("r-genomation" ,r-genomation)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-stringr" ,r-stringr)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-heatmaply" ,r-heatmaply)
+ ("r-htmlwidgets" ,r-htmlwidgets)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-plotly" ,r-plotly)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("python-wrapper" ,python-wrapper)
+ ("python-pyyaml" ,python-pyyaml)
+ ("python-magic" ,python-magic)
+ ("python-xlrd" ,python-xlrd)
+ ("trim-galore" ,trim-galore)
+ ("macs" ,macs)
+ ("multiqc" ,multiqc)
+ ("perl" ,perl)
+ ("ghc-pandoc" ,ghc-pandoc-1)
+ ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
+ ("fastqc" ,fastqc)
+ ("bowtie" ,bowtie)
+ ("idr" ,idr)
+ ("snakemake" ,snakemake)
+ ("samtools" ,samtools)
+ ("bedtools" ,bedtools)
+ ("kentutils" ,kentutils)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+ (synopsis "Analysis pipeline for ChIP sequencing experiments")
+ (description "PiGX ChIPseq is an analysis pipeline for preprocessing, peak
+calling and reporting for ChIP sequencing experiments. It is easy to use and
+produces high quality reports. The inputs are reads files from the sequencing
+experiment, and a configuration file which describes the experiment. In
+addition to quality control of the experiment, the pipeline enables to set up
+multiple peak calling analysis and allows the generation of a UCSC track hub
+in an easily configurable manner.")
+ (license license:gpl3+)))
+
+(define-public pigx-bsseq
+ (package
+ (name "pigx-bsseq")
+ (version "0.0.8")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
+ "releases/download/v" version
+ "/pigx_bsseq-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0irlnlhhw9fd4ha7hksrxn3y7j76mz5qq1wjswbs9p364laqg69y"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'check 'set-timezone
+ ;; The readr package is picky about timezones.
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "TZ" "UTC+1")
+ (setenv "TZDIR"
+ (string-append (assoc-ref inputs "tzdata")
+ "/share/zoneinfo"))
+ #t))
+ (add-after 'install 'wrap-executable
+ ;; Make sure the executable finds all R modules.
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (wrap-program (string-append out "/bin/pigx-bsseq")
+ `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
+ `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
+ #t)))))
+ (native-inputs
+ `(("tzdata" ,tzdata)))
+ (inputs
+ `(("coreutils" ,coreutils)
+ ("sed" ,sed)
+ ("grep" ,grep)
+ ("r-minimal" ,r-minimal)
+ ("r-annotationhub" ,r-annotationhub)
+ ("r-dt" ,r-dt)
+ ("r-genomation" ,r-genomation)
+ ("r-methylkit" ,r-methylkit)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-bookdown" ,r-bookdown)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggbio" ,r-ggbio)
+ ("ghc-pandoc" ,ghc-pandoc-1)
+ ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
+ ("python-wrapper" ,python-wrapper)
+ ("python-pyyaml" ,python-pyyaml)
+ ("snakemake" ,snakemake)
+ ("bismark" ,bismark)
+ ("fastqc" ,fastqc)
+ ("bowtie" ,bowtie)
+ ("trim-galore" ,trim-galore)
+ ("cutadapt" ,cutadapt)
+ ("samtools" ,samtools)))
+ (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+ (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports")
+ (description "PiGx BSseq is a data processing pipeline for raw fastq read
+data of bisulfite experiments; it produces reports on aggregate methylation
+and coverage and can be used to produce information on differential
+methylation and segmentation.")
+ (license license:gpl3+)))
+
+(define-public pigx-scrnaseq
+ (package
+ (name "pigx-scrnaseq")
+ (version "0.0.4")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
+ "releases/download/v" version
+ "/pigx_scrnaseq-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1pvjm6f3mascprs65vflggwwg5v925knvgal7k7a6nnlmw5qndrf"))))
+ (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"))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'install 'wrap-executable
+ ;; Make sure the executable finds all R modules.
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (wrap-program (string-append out "/bin/pigx-scrnaseq")
+ `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
+ `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
+ #t)))))
+ (inputs
+ `(("coreutils" ,coreutils)
+ ("perl" ,perl)
+ ("dropseq-tools" ,dropseq-tools)
+ ("fastqc" ,fastqc)
+ ("java-picard" ,java-picard)
+ ("java" ,icedtea-8)
+ ("python-wrapper" ,python-wrapper)
+ ("python-pyyaml" ,python-pyyaml)
+ ("python-pandas" ,python-pandas)
+ ("python-numpy" ,python-numpy)
+ ("python-loompy" ,python-loompy)
+ ("ghc-pandoc" ,ghc-pandoc-1)
+ ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
+ ("snakemake" ,snakemake)
+ ("star" ,star)
+ ("r-minimal" ,r-minimal)
+ ("r-argparser" ,r-argparser)
+ ("r-cowplot" ,r-cowplot)
+ ("r-data-table" ,r-data-table)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+ ("r-dplyr" ,r-dplyr)
+ ("r-dropbead" ,r-dropbead)
+ ("r-dt" ,r-dt)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfiles" ,r-genomicfiles)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-hdf5array" ,r-hdf5array)
+ ("r-pheatmap" ,r-pheatmap)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-rtsne" ,r-rtsne)
+ ("r-scater" ,r-scater)
+ ("r-scran" ,r-scran)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-stringr" ,r-stringr)
+ ("r-yaml" ,r-yaml)))
+ (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+ (synopsis "Analysis pipeline for single-cell RNA sequencing experiments")
+ (description "PiGX scRNAseq is an analysis pipeline for preprocessing and
+quality control for single cell RNA sequencing experiments. The inputs are
+read files from the sequencing experiment, and a configuration file which
+describes the experiment. It produces processed files for downstream analysis
+and interactive quality reports. The pipeline is designed to work with UMI
+based methods.")
+ (license license:gpl3+)))
+
+(define-public pigx
+ (package
+ (name "pigx")
+ (version "0.0.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/BIMSBbioinfo/pigx/"
+ "releases/download/v" version
+ "/pigx-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0sb708sl42h3s5z872jb1w70bbqplwapnsc1wm27zcsvi7li4gw8"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("python" ,python)
+ ("pigx-bsseq" ,pigx-bsseq)
+ ("pigx-chipseq" ,pigx-chipseq)
+ ("pigx-rnaseq" ,pigx-rnaseq)
+ ("pigx-scrnaseq" ,pigx-scrnaseq)))
+ (home-page "http://bioinformatics.mdc-berlin.de/pigx/")
+ (synopsis "Analysis pipelines for genomics")
+ (description "PiGx is a collection of genomics pipelines. It includes the
+following pipelines:
+
+@itemize
+@item PiGx BSseq for raw fastq read data of bisulfite experiments
+@item PiGx RNAseq for RNAseq samples
+@item PiGx scRNAseq for single cell dropseq analysis
+@item PiGx ChIPseq for reads from ChIPseq experiments
+@end itemize
+
+All pipelines are easily configured with a simple sample sheet and a
+descriptive settings file. The result is a set of comprehensive, interactive
+HTML reports with interesting findings about your samples.")
+ (license license:gpl3+)))
+
+(define-public r-diversitree
+ (package
+ (name "r-diversitree")
+ (version "0.9-10")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "diversitree" version))
+ (sha256
+ (base32
+ "0gh4rcrp0an3jh8915i1fsxlgyfk7njywgbd5ln5r2jhr085kpz7"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-desolve" ,r-desolve)
+ ("r-rcpp" ,r-rcpp)
+ ("r-suplex" ,r-subplex)))
+ (home-page "https://www.zoology.ubc.ca/prog/diversitree")
+ (synopsis "Comparative 'phylogenetic' analyses of diversification")
+ (description "This package contains a number of comparative \"phylogenetic\"
+methods, mostly focusing on analysing diversification and character evolution.
+Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
+and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
+Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
+include Markov models of discrete and continuous trait evolution and constant
+rate speciation and extinction.")
+ (license license:gpl2+)))
HCoop / jackhill / guix / guix.git / blobdiff