diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 184 |
1 files changed, 148 insertions, 36 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 982cb7a984..4481235c78 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -84,6 +84,7 @@ #:use-module (gnu packages jemalloc) #:use-module (gnu packages dlang) #:use-module (gnu packages linux) + #:use-module (gnu packages lisp) #:use-module (gnu packages logging) #:use-module (gnu packages machine-learning) #:use-module (gnu packages man) @@ -1384,6 +1385,46 @@ gapped, local, and paired-end alignment modes.") (supported-systems '("x86_64-linux")) (license license:gpl3+))) +(define-public bowtie1 + (package + (name "bowtie1") + (version "1.2.2") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/bowtie-bio/bowtie/" + version "/bowtie-" version "-src.zip")) + (sha256 + (base32 + "1jl2cj9bz8lwz8dwnxbycn8yp8g4kky62fkcxifyf1ri0y6n2vc0")) + (modules '((guix build utils))) + (snippet + '(substitute* "Makefile" + ;; replace BUILD_HOST and BUILD_TIME for deterministic build + (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") + (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ; no "check" target + #:make-flags + (list "all" + (string-append "prefix=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (inputs + `(("tbb" ,tbb) + ("zlib" ,zlib))) + (supported-systems '("x86_64-linux")) + (home-page "http://bowtie-bio.sourceforge.net/index.shtml") + (synopsis "Fast aligner for short nucleotide sequence reads") + (description + "Bowtie is a fast, memory-efficient short read aligner. It aligns short +DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp +reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to +keep its memory footprint small: typically about 2.2 GB for the human +genome (2.9 GB for paired-end).") + (license license:artistic2.0))) + (define-public tophat (package (name "tophat") @@ -6240,6 +6281,48 @@ sequence.") (supported-systems '("i686-linux" "x86_64-linux")) (license license:bsd-3))) +(define-public r-scde + (package + (name "r-scde") + (version "1.99.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hms-dbmi/scde.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10na2gyka24mszdxf92wz9h2c13hdf1ww30c68gfsw53lvvhhhxb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-mgcv" ,r-mgcv) + ("r-rook" ,r-rook) + ("r-rjson" ,r-rjson) + ("r-cairo" ,r-cairo) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-edger" ,r-edger) + ("r-quantreg" ,r-quantreg) + ("r-nnet" ,r-nnet) + ("r-rmtstat" ,r-rmtstat) + ("r-extremes" ,r-extremes) + ("r-pcamethods" ,r-pcamethods) + ("r-biocparallel" ,r-biocparallel) + ("r-flexmix" ,r-flexmix))) + (home-page "https://hms-dbmi.github.io/scde/") + (synopsis "R package for analyzing single-cell RNA-seq data") + (description "The SCDE package implements a set of statistical methods for +analyzing single-cell RNA-seq data. SCDE fits individual error models for +single-cell RNA-seq measurements. These models can then be used for +assessment of differential expression between groups of cells, as well as +other types of analysis. The SCDE package also contains the pagoda framework +which applies pathway and gene set overdispersion analysis to identify aspects +of transcriptional heterogeneity among single cells.") + ;; See https://github.com/hms-dbmi/scde/issues/38 + (license license:gpl2))) + (define-public r-centipede (package (name "r-centipede") @@ -7127,28 +7210,6 @@ checks on R packages that are to be submitted to the Bioconductor repository.") that accept short and long options.") (license license:gpl2+))) -(define-public r-dnacopy - (package - (name "r-dnacopy") - (version "1.56.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "DNAcopy" version)) - (sha256 - (base32 - "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82")))) - (properties - `((upstream-name . "DNAcopy"))) - (build-system r-build-system) - (inputs - `(("gfortran" ,gfortran))) - (home-page "https://bioconductor.org/packages/DNAcopy") - (synopsis "Implementation of a circular binary segmentation algorithm") - (description "This package implements the circular binary segmentation (CBS) -algorithm to segment DNA copy number data and identify genomic regions with -abnormal copy number.") - (license license:gpl2+))) - (define-public r-s4vectors (package (name "r-s4vectors") @@ -11613,7 +11674,7 @@ Browser.") (define-public bismark (package (name "bismark") - (version "0.19.1") + (version "0.20.1") (source (origin (method git-fetch) @@ -11623,18 +11684,25 @@ Browser.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "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)))) + "0xchm3rgilj6vfjnyzfzzymfd7djr64sbrmrvs3njbwi66jqbzw9")))) (build-system perl-build-system) (arguments `(#:tests? #f ; there are no tests + #:modules ((guix build utils) + (ice-9 popen) + (srfi srfi-26) + (guix build perl-build-system)) #:phases (modify-phases %standard-phases + ;; The bundled plotly.js is minified. + (add-after 'unpack 'replace-plotly.js + (lambda* (#:key inputs #:allow-other-keys) + (let* ((file (assoc-ref inputs "plotly.js")) + (installed "plotly/plotly.js")) + (let ((minified (open-pipe* OPEN_READ "uglify-js" file))) + (call-with-output-file installed + (cut dump-port minified <>)))) + #t)) (delete 'configure) (delete 'build) (replace 'install @@ -11653,10 +11721,11 @@ Browser.") "deduplicate_bismark" "filter_non_conversion" "bam2nuc" - "bismark2summary"))) + "bismark2summary" + "NOMe_filtering"))) (substitute* "bismark2report" - (("\\$RealBin/bismark_sitrep") - (string-append share "/bismark_sitrep"))) + (("\\$RealBin/plotly") + (string-append share "/plotly"))) (mkdir-p share) (mkdir-p docdir) (mkdir-p bin) @@ -11665,8 +11734,8 @@ Browser.") (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")) + (copy-recursively "plotly" + (string-append share "/plotly")) ;; Fix references to gunzip (substitute* (map (lambda (file) @@ -11677,7 +11746,18 @@ Browser.") "/bin/gunzip -c"))) #t)))))) (inputs - `(("gzip" ,gzip))) + `(("gzip" ,gzip) + ("perl-carp" ,perl-carp) + ("perl-getopt-long" ,perl-getopt-long))) + (native-inputs + `(("plotly.js" + ,(origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/plotly/plotly.js/" + "v1.39.4/dist/plotly.js")) + (sha256 + (base32 "138mwsr4nf5qif4mrxx286mpnagxd1xwl6k8aidrjgknaqg88zyr")))) + ("uglify-js" ,uglify-js))) (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 @@ -13135,6 +13215,38 @@ descriptive settings file. The result is a set of comprehensive, interactive HTML reports with interesting findings about your samples.") (license license:gpl3+))) +(define-public genrich + (package + (name "genrich") + (version "0.5") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jsh58/Genrich.git") + (commit (string-append "v" version)))) + (sha256 + (base32 + "0x0q6z0208n3cxzqjla4rgjqpyqgwpmz27852lcvzkzaigymq4zp")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are none + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (install-file "Genrich" (string-append (assoc-ref outputs "out") "/bin")) + #t))))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/jsh58/Genrich") + (synopsis "Detecting sites of genomic enrichment") + (description "Genrich is a peak-caller for genomic enrichment +assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated +following the assay and produces a file detailing peaks of significant +enrichment.") + (license license:expat))) + (define-public mantis (let ((commit "4ffd171632c2cb0056a86d709dfd2bf21bc69b84") (revision "1")) |