diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 41 |
1 files changed, 25 insertions, 16 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 32f9b72d99..d4380f86ac 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3632,7 +3632,7 @@ data.") (define-public kaiju (package (name "kaiju") - (version "1.5.0") + (version "1.6.2") (source (origin (method url-fetch) (uri (string-append @@ -3641,7 +3641,7 @@ data.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0afbfalfw9y39bkwnqjrh9bghs118ws1pzj5h8l0nblgn3mbjdks")))) + "1kdn4rxs0kr9ibmrgrfcci71aa6j6gr71dbc8pff7731rpab6kj7")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; There are no tests. @@ -3659,7 +3659,8 @@ data.") (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 @@ -6077,14 +6078,14 @@ data types as well.") (define-public r-annotate (package (name "r-annotate") - (version "1.56.1") + (version "1.56.2") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "14c5xd9kasvcwg5gbjys2c1vizxhlqlzxakqc2kml0kw97hmx0rq")))) + "0ybg9k1s289h15nj1kp9821i1rsk1gkn8i8blplmk7gsgpbw1f42")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -6886,8 +6887,7 @@ also known as views, in a controlled vocabulary.") ("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 @@ -8526,14 +8526,14 @@ library implementing most of the pipeline's features.") (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) @@ -8543,7 +8543,6 @@ library implementing most of the pipeline's features.") ("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) @@ -12757,7 +12756,7 @@ expression report comparing samples in an easily configurable manner.") (define-public pigx-chipseq (package (name "pigx-chipseq") - (version "0.0.8") + (version "0.0.10") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" @@ -12765,7 +12764,7 @@ expression report comparing samples in an easily configurable manner.") "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "1plw0bz0b7flj0g9irbn8n520005lmajkiq5flpizzapsl0a0r9g")))) + "13w99bkr0w4j28ms0yzpl1x6fkpdqay0vh495q3x20bcilsjwnf1")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; parts of the tests rely on access to the network @@ -12780,24 +12779,34 @@ expression report comparing samples in an easily configurable manner.") `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) #t))))) (inputs - `(("r-minimal" ,r-minimal) + `(("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-rcas" ,r-rcas) + ("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-magic" ,python-magic) ("python-pyyaml" ,python-pyyaml) + ("python-magic" ,python-magic) ("python-xlrd" ,python-xlrd) - ("snakemake" ,snakemake) ("trim-galore" ,trim-galore) ("macs" ,macs) ("multiqc" ,multiqc) |