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authorMark H Weaver <mhw@netris.org>2019-09-06 20:46:00 -0400
committerMark H Weaver <mhw@netris.org>2019-09-06 20:46:00 -0400
commit65542a8852759f35e19959149ac92297c8b54be5 (patch)
treebc8f398c7b10a4725b20aa59ab1452d30f358ea3 /gnu/packages/bioinformatics.scm
parentbc60349b5bc58a0b803df5adce1de6db82453744 (diff)
parentf66aee3d0d2f573187ed5d44ae7c13d73cd4097a (diff)
downloadpatches-65542a8852759f35e19959149ac92297c8b54be5.tar
patches-65542a8852759f35e19959149ac92297c8b54be5.tar.gz
Merge branch 'master' into core-updates
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm88
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)))