diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 88 |
1 files changed, 62 insertions, 26 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b2953fddbf..e158bd3af7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -77,9 +77,9 @@ #:use-module (gnu packages groff) #:use-module (gnu packages guile) #:use-module (gnu packages guile-xyz) - #:use-module (gnu packages haskell) #:use-module (gnu packages haskell-check) #:use-module (gnu packages haskell-web) + #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) @@ -1758,8 +1758,8 @@ well as many of the command line options.") (add-after 'unpack 'keep-references-to-bwa (lambda* (#:key inputs #:allow-other-keys) (substitute* "bwameth.py" - (("bwa mem") - (string-append (which "bwa") " mem")) + (("bwa (mem|index)" _ command) + (string-append (which "bwa") " " command)) ;; There's an ill-advised check for "samtools" on PATH. (("^checkX.*") "")) #t))))) @@ -2344,16 +2344,16 @@ other types of unwanted sequence from high-throughput sequencing reads.") (define-public libbigwig (package (name "libbigwig") - (version "0.4.2") + (version "0.4.4") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/dpryan79/libBigWig.git") (commit version))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 - "0h2smg24v5srdcqzrmz2g23cmlp4va465mgx8r2z571sfz8pv454")))) + "09693dmf1scdac5pyq6qyn8b4mcipvnmc370k9a5z41z81m3dcsj")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -7367,13 +7367,13 @@ S4Vectors package itself.") (define-public r-iranges (package (name "r-iranges") - (version "2.18.1") + (version "2.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "1d64sh43pfc9vj2l7y7x6sb44l67wlnn3dzygp7ws0smn06mardq")))) + "0dc35844c1mfj07hvy6yn4wag6qdggbgl9gjcg3wpkh9hkm60a5n")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -7620,13 +7620,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.46.0") + (version "1.46.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "0lfq5668a6sq4kqhxx78hl3jcaqdsaaliiybl9xyya2scdk8c29c")))) + "13nanz4nzy0mcda8ljz2g8d81hpqfz6jky7ydz5hpk0g2264b9ga")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -7647,13 +7647,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.40.3") + (version "2.40.4") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "022m1r44s00c5k9bmv0lr22lcn662nhc91aazvv0yyysxjamyf60")))) + "0dj51qkxm7bh24b3bs1di7lic6zgi7g5gf9iqkqhrwkbm7sqvn0v")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -7872,13 +7872,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.44.2") + (version "1.44.3") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "03b4rfsbzjjf5kxcsjv7kq8hrsgcvz9rfzcn2v7fx3nr818pbb8s")))) + "091zydz1zpz519ha0jkbvzrhxjvw5r2963qz9grmvl2jd8girvcg")))) (build-system r-build-system) (arguments `(#:phases @@ -9446,13 +9446,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "3.0.2") + (version "3.1.0") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "016fgcmjz3sjfxdvam5hd7mdxpmpnc7f6p5zqlh97m21dgn5vpqn")))) + "0icxndnnkkmmr9hhd01dv3w8pih7x9r0rlp3fq9pk3qajp9gmlyq")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -9469,6 +9469,7 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") ("r-igraph" ,r-igraph) ("r-irlba" ,r-irlba) ("r-kernsmooth" ,r-kernsmooth) + ("r-leiden" ,r-leiden) ("r-lmtest" ,r-lmtest) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) @@ -9479,6 +9480,7 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") ("r-rann" ,r-rann) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) + ("r-rcppannoy" ,r-rcppannoy) ("r-rcppeigen" ,r-rcppeigen) ("r-rcppprogress" ,r-rcppprogress) ("r-reticulate" ,r-reticulate) @@ -9489,7 +9491,8 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") ("r-scales" ,r-scales) ("r-sctransform" ,r-sctransform) ("r-sdmtools" ,r-sdmtools) - ("r-tsne" ,r-tsne))) + ("r-tsne" ,r-tsne) + ("r-uwot" ,r-uwot))) (home-page "http://www.satijalab.org/seurat") (synopsis "Seurat is an R toolkit for single cell genomics") (description @@ -10176,22 +10179,24 @@ by Ernst and Kellis.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.14.0") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "0lraxhq9ny3468534klrl64nx0dpaf9cbd5bir6m5qma8j7kfnyd")))) + "0xx04cghx6ads1ackwnw3z0gf72qv461nznzmcnkgmp7w5n9m2af")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) - ("r-erma" ,r-erma) + ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75) + ("r-ensembldb" ,r-ensembldb) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfiles" ,r-genomicfiles) ("r-go-db" ,r-go-db) ("r-homo-sapiens" ,r-homo-sapiens) + ("r-httr" ,r-httr) ("r-matrix" ,r-matrix) ("r-rsamtools" ,r-rsamtools) ("r-snpstats" ,r-snpstats) @@ -13412,8 +13417,7 @@ bgzipped text file that contains a pair of genomic coordinates per line.") "0y5zyjksj1rdglj601xd2bbni5abhdh622y3ck76chyzxz9z4rx8")))) (build-system python-build-system) (propagated-inputs - `(("python-setuptools" ,python-setuptools) - ("python-six" ,python-six))) + `(("python-six" ,python-six))) (home-page "http://mattshirley.com") (synopsis "Random access to fasta subsequences") (description @@ -14653,16 +14657,14 @@ proximity within a reference genome.") "08y3vz1vcx09whmbsn722lcs6jl9wyrh9i4p3k8j4cb1i32bij4a")))) (build-system python-build-system) (inputs - `(("python-setuptools" ,python-setuptools) - ("python-pandas" ,python-pandas) + `(("python-pandas" ,python-pandas) ("python-future" ,python-future) ("python-scipy" ,python-scipy) ("python-matplotlib" ,python-matplotlib) ("python-regex" ,python-regex) ("python-pysam" ,python-pysam))) (native-inputs - `(("python-setuptools" ,python-setuptools) - ("python-cython" ,python-cython))) + `(("python-cython" ,python-cython))) (home-page "https://github.com/CGATOxford/UMI-tools") (synopsis "Tools for analyzing unique modular identifiers") (description "This package provides tools for dealing with @dfn{Unique @@ -15215,3 +15217,37 @@ indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.") (license license:expat)))) + +(define-public samblaster + (package + (name "samblaster") + (version "0.1.24") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/GregoryFaust/samblaster.git") + (commit (string-append "v." version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0iv2ddfw8363vb2x8gr3p8g88whb6mb9m0pf71i2cqsbv6jghap7")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are none + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (install-file "samblaster" + (string-append (assoc-ref outputs "out") "/bin")) + #t))))) + (home-page "https://github.com/GregoryFaust/samblaster") + (synopsis "Mark duplicates in paired-end SAM files") + (description "Samblaster is a fast and flexible program for marking +duplicates in read-id grouped paired-end SAM files. It can also optionally +output discordant read pairs and/or split read mappings to separate SAM files, +and/or unmapped/clipped reads to a separate FASTQ file. When marking +duplicates, samblaster will require approximately 20MB of memory per 1M read +pairs.") + (license license:expat))) |