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Merge branch 'master' into core-updates

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Mark H Weaver 2018-03-20 00:49:05 -04:00
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100 changed files with 1294 additions and 694 deletions
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gnu/packages/bioinformatics.scm
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@ -8448,7 +8448,7 @@ paired-end data.")
("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)
@ -11521,7 +11521,7 @@ Browser.")
(delete 'configure)
(delete 'build)
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out")
"/bin"))
(docdir (string-append (assoc-ref outputs "out")
@ -11544,7 +11544,16 @@ Browser.")
scripts)
(for-each (lambda (file) (install-file file docdir))
docs)
;; 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
@ -12729,8 +12738,8 @@ once. This package provides tools to perform Drop-seq analyses.")
("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/")
@ -12746,7 +12755,7 @@ expression report comparing samples in an easily configurable manner.")
(define-public pigx-chipseq
(package
(name "pigx-chipseq")
(version "0.0.2")
(version "0.0.8")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
@ -12754,10 +12763,11 @@ expression report comparing samples in an easily configurable manner.")
"/pigx_chipseq-" version ".tar.gz"))
(sha256
(base32
"1jliwhifnjgl9x0z730bzpxswi2s84fyg5y8cagbyzpw509452f5"))))
"1plw0bz0b7flj0g9irbn8n520005lmajkiq5flpizzapsl0a0r9g"))))
(build-system gnu-build-system)
(arguments
`(#:phases
`(#: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.
@ -12782,13 +12792,16 @@ expression report comparing samples in an easily configurable manner.")
("r-ggplot2" ,r-ggplot2)
("r-plotly" ,r-plotly)
("python-wrapper" ,python-wrapper)
("python-magic" ,python-magic)
("python-pyyaml" ,python-pyyaml)
("python-xlrd" ,python-xlrd)
("snakemake" ,snakemake)
("trim-galore" ,trim-galore)
("macs" ,macs)
("multiqc" ,multiqc)
("perl" ,perl)
("ghc-pandoc" ,ghc-pandoc)
("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
("ghc-pandoc" ,ghc-pandoc-1)
("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
("fastqc" ,fastqc)
("bowtie" ,bowtie)
("idr" ,idr)
@ -12812,7 +12825,7 @@ in an easily configurable manner.")
(define-public pigx-bsseq
(package
(name "pigx-bsseq")
(version "0.0.5")
(version "0.0.7")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
@ -12820,7 +12833,7 @@ in an easily configurable manner.")
"/pigx_bsseq-" version ".tar.gz"))
(sha256
(base32
"1h8ma99vi7hs83nafvjpq8jmaq9977j3n11c4zd95hai0cf7zxmp"))))
"0pw797gxx6x1n56lyrvglj7q5hqq4ylfqkvlcrzq1z3j5lxcyl69"))))
(build-system gnu-build-system)
(arguments
`(#:phases
@ -12844,7 +12857,10 @@ in an easily configurable manner.")
(native-inputs
`(("tzdata" ,tzdata)))
(inputs
`(("r-minimal" ,r-minimal)
`(("coreutils" ,coreutils)
("sed" ,sed)
("grep" ,grep)
("r-minimal" ,r-minimal)
("r-annotationhub" ,r-annotationhub)
("r-dt" ,r-dt)
("r-genomation" ,r-genomation)
@ -12854,8 +12870,8 @@ in an easily configurable manner.")
("r-bookdown" ,r-bookdown)
("r-ggplot2" ,r-ggplot2)
("r-ggbio" ,r-ggbio)
("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)
("snakemake" ,snakemake)
@ -12876,7 +12892,7 @@ methylation and segmentation.")
(define-public pigx-scrnaseq
(package
(name "pigx-scrnaseq")
(version "0.0.2")
(version "0.0.3")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
@ -12884,7 +12900,7 @@ methylation and segmentation.")
"/pigx_scrnaseq-" version ".tar.gz"))
(sha256
(base32
"03gwp83823ji59y6nvyz89i4yd3faaqpc3791qia71i91470vfsg"))))
"12qdq0nj1wdkyighdxj6924bmbpd1a0b3gam6w64l4hiqrv5sijz"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
@ -12903,7 +12919,9 @@ methylation and segmentation.")
`("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
#t)))))
(inputs
`(("dropseq-tools" ,dropseq-tools)
`(("coreutils" ,coreutils)
("perl" ,perl)
("dropseq-tools" ,dropseq-tools)
("fastqc" ,fastqc)
("java-picard" ,java-picard)
("java" ,icedtea-8)
@ -12912,8 +12930,8 @@ methylation and segmentation.")
("python-pandas" ,python-pandas)
("python-numpy" ,python-numpy)
("python-loompy" ,python-loompy)
("ghc-pandoc" ,ghc-pandoc)
("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
("ghc-pandoc" ,ghc-pandoc-1)
("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
("snakemake" ,snakemake)
("star" ,star)
("r-minimal" ,r-minimal)
@ -12953,7 +12971,7 @@ based methods.")
(define-public pigx
(package
(name "pigx")
(version "0.0.1")
(version "0.0.2")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx/"
@ -12961,7 +12979,7 @@ based methods.")
"/pigx-" version ".tar.gz"))
(sha256
(base32
"1nxb2hbp40yg3j7n56k4dhsd2fl1j8g0wpiiln56prqzljwnlgmf"))))
"0sb708sl42h3s5z872jb1w70bbqplwapnsc1wm27zcsvi7li4gw8"))))
(build-system gnu-build-system)
(inputs
`(("python" ,python)