From dddbc90c648a569ed3f6dcf8678cb94e63a8302f Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Thu, 29 Aug 2019 21:56:35 -0400 Subject: gnu: Move non-compilers out of haskell.scm. * gnu/packages/haskell.scm (ghc-abstract-deque, ghc-abstract-par, ghc-adjunctions, ghc-aeson-compat, ghc-alex, ghc-alsa-core, ghc-annotated-wl-pprint, ghc-ansi-terminal, ghc-ansi-wl-pprint, ghc-appar, ghc-async, ghc-atomic-write, ghc-attoparsec, ghc-attoparsec-bootstrap, ghc-attoparsec-iso8601, ghc-auto-update, ghc-aws, ghc-base16-bytestring, ghc-base64-bytestring, ghc-base-compat, ghc-basement, ghc-base-orphans, ghc-base-prelude, ghc-base-unicode-symbols, ghc-bifunctors, ghc-bindings-dsl, ghc-blaze-builder, ghc-blaze-markup, ghc-bloomfilter, ghc-boxes, ghc-byteable, ghc-byteorder, ghc-bytes, ghc-bytestring-builder, ghc-bytestring-handle, ghc-bytestring-lexing, ghc-bzlib-conduit, ghc-c2hs, ghc-cairo, ghc-call-stack, ghc-call-stack-boot, ghc-case-insensitive, ghc-cereal, ghc-cereal-conduit, ghc-cgi, ghc-charset, ghc-chart, ghc-chart-cairo, ghc-chasingbottoms, ghc-cheapskate, ghc-chell, ghc-chell-quickcheck, ghc-chunked-data, ghc-clock, ghc-clock-bootstrap, ghc-cmark, ghc-cmark-gfm, ghc-cmdargs, ghc-code-page, ghc-colour, ghc-comonad, ghc-concatenative, ghc-concurrent-output, ghc-conduit, ghc-conduit-algorithms, ghc-conduit-combinators, ghc-conduit-extra, ghc-configurator, ghc-connection, ghc-constraints, ghc-contravariant, ghc-contravariant-extras, ghc-convertible, ghc-data-accessor, ghc-data-accessor-transformers, ghc-data-default, ghc-data-default-class, ghc-data-default-instances-base, ghc-data-default-instances-containers, ghc-data-default-instances-dlist, ghc-data-default-instances-old-locale, ghc-data-hash, ghc-data-ordlist, ghc-deepseq-generics, ghc-descriptive, ghc-diff, ghc-disk-free-space, ghc-distributive, ghc-dlist, ghc-doctemplates, ghc-doctest, ghc-double-conversion, ghc-easy-file, ghc-easyplot, ghc-echo, ghc-edisonapi, ghc-edisoncore, ghc-edit-distance, ghc-either, ghc-email-validate, ghc-enclosed-exceptions, ghc-equivalence, ghc-erf, ghc-errorcall-eq-instance, ghc-errors, ghc-esqueleto, ghc-exactprint, ghc-exceptions, ghc-executable-path, ghc-extensible-exceptions, ghc-extra, ghc-fail, ghc-fast-logger, ghc-feed, ghc-fgl, ghc-fgl-arbitrary, ghc-file-embed, ghc-filemanip, ghc-findbin, ghc-fingertree, ghc-fixed, ghc-foldl, ghc-foundation, ghc-free, ghc-fsnotify, ghc-generic-deriving, ghc-generics-sop, ghc-geniplate-mirror, ghc-genvalidity, ghc-genvalidity-property, ghc-gitrev, ghc-glob, ghc-gluraw, ghc-glut, ghc-gnuplot, ghc-graphviz, ghc-gtk2hs-buildtools, ghc-hackage-security, ghc-haddock, ghc-haddock-api, ghc-haddock-library, ghc-half, ghc-happy, ghc-hashable, ghc-hashable-bootstrap, ghc-hashable-time, ghc-hashtables, ghc-haskell-lexer, ghc-haskell-src, ghc-haskell-src-exts, ghc-haskell-src-exts-util, ghc-haskell-src-meta, ghc-hasktags, ghc-hex, ghc-highlighting-kate, ghc-hindent, ghc-hinotify, ghc-hmatrix, ghc-hmatrix-gsl, ghc-hmatrix-gsl-stats, ghc-hmatrix-special, ghc-hostname, ghc-hourglass, ghc-hpack, ghc-hs-bibutils, ghc-hslogger, ghc-hslua, ghc-hslua-module-text, ghc-http-api-data, ghc-ieee754, ghc-ifelse, ghc-indents, ghc-inline-c, ghc-inline-c-cpp, ghc-integer-logarithms, ghc-integer-logarithms-bootstrap, ghc-interpolate, ghc-intervalmap, ghc-invariant, ghc-iproute, ghc-iwlib, ghc-json, ghc-juicypixels, ghc-kan-extensions, ghc-language-c, ghc-language-haskell-extract, ghc-lens, ghc-libffi, ghc-libmpd, ghc-libxml, ghc-lifted-async, ghc-lifted-base, ghc-linear, ghc-logging-facade, ghc-logict, ghc-lzma, ghc-lzma-conduit, ghc-markdown-unlit, ghc-math-functions, ghc-megaparsec, ghc-memory, ghc-memotrie, ghc-microlens, ghc-microlens-ghc, ghc-microlens-mtl, ghc-microlens-platform, ghc-microlens-th, ghc-missingh, ghc-mmap, ghc-mmorph, ghc-mockery, ghc-monad-control, ghc-monad-logger, ghc-monad-loops, ghc-monad-par, ghc-monad-par-extras, ghc-monadplus, ghc-monadrandom, ghc-monads-tf, ghc-mono-traversable, ghc-murmur-hash, ghc-mwc-random, ghc-nats, ghc-nats-bootstrap, ghc-network, ghc-network-info, ghc-network-uri, ghc-newtype-generics, ghc-objectname, ghc-old-locale, ghc-old-time, ghc-opengl, ghc-openglraw, ghc-operational, ghc-options, ghc-optparse-applicative, ghc-pandoc, ghc-pandoc-citeproc, ghc-pandoc-types, ghc-parallel, ghc-parsec-numbers, ghc-parser-combinators, ghc-parsers, ghc-path, ghc-path-io, ghc-paths, ghc-patience, ghc-pcre-light, ghc-persistent, ghc-persistent-sqlite, ghc-persistent-template, ghc-polyparse, ghc-pqueue, ghc-prelude-extras, ghc-pretty-hex, ghc-pretty-show, ghc-primitive, ghc-profunctors, ghc-psqueues, ghc-random, ghc-raw-strings-qq, ghc-rebase, ghc-reducers, ghc-refact, ghc-reflection, ghc-regex, ghc-regex-applicative, ghc-regex-base, ghc-regex-compat, ghc-regex-compat-tdfa, ghc-regex-pcre-builtin, ghc-regex-posix, ghc-regex-tdfa, ghc-regex-tdfa-text, ghc-rerebase, ghc-resolv, ghc-resource-pool, ghc-resourcet, ghc-rfc5051, ghc-rio, ghc-safe, ghc-safe-exceptions, ghc-safeio, ghc-safesemaphore, ghc-sandi, ghc-scientific, ghc-scientific-bootstrap, ghc-sdl, ghc-sdl-image, ghc-sdl-mixer, ghc-securemem, ghc-semigroupoids, ghc-semigroups, ghc-semigroups-bootstrap, ghc-setenv, ghc-setlocale, ghc-shakespeare, ghc-shelly, ghc-silently, ghc-simple-reflect, ghc-simple-sendfile, ghc-skylighting-core, ghc-skylighting, ghc-smallcheck, ghc-socks, ghc-split, ghc-statevar, ghc-statistics, ghc-stm-chans, ghc-stm-conduit, ghc-stmonadtrans, ghc-storable-complex, ghc-streaming-commons, ghc-strict, ghc-stringbuilder, ghc-string-qq, ghc-stringsearch, ghc-stylish-haskell, ghc-syb, ghc-system-fileio, ghc-system-filepath, ghc-tagged, ghc-tar, ghc-temporary, ghc-temporary-rc, ghc-terminal-size, ghc-texmath, ghc-text-binary, ghc-tf-random, ghc-th-abstraction, ghc-th-expand-syns, ghc-th-lift, ghc-th-lift-instances, ghc-th-orphans, ghc-th-reify-many, ghc-time-locale-compat, ghc-tldr, ghc-transformers-base, ghc-transformers-compat, ghc-tree-diff, ghc-trifecta, ghc-tuple-th, ghc-typed-process, ghc-unbounded-delays, ghc-unexceptionalio, ghc-union-find, ghc-uniplate, ghc-unix-compat, ghc-unix-time, ghc-unliftio, ghc-unliftio-core, ghc-unordered-containers, ghc-unordered-containers-bootstrap, ghc-uri-bytestring, ghc-utf8-string, ghc-utility-ht, ghc-uuid, ghc-uuid-types, ghc-validation, ghc-validity, ghc-vault, ghc-vector, ghc-vector-algorithms, ghc-vector-binary-instances, ghc-vector-builder, ghc-vector-th-unbox, ghc-void, ghc-wave, ghc-wcwidth, ghc-wcwidth-bootstrap, ghc-weigh, ghc-wl-pprint, ghc-wl-pprint-annotated, ghc-wl-pprint-text, ghc-word8, ghc-x11, ghc-x11-xft, ghc-xdg-basedir, ghc-xml, ghc-xml-conduit, ghc-xml-types, ghc-yaml, ghc-zip-archive, ghc-zlib): Move variables from here... * gnu/packages/haskell-xyz.scm: ...to here. * gnu/packages/agda.scm, gnu/packages/bioconductor.scm, gnu/packages/bioinformatics.scm, gnu/packages/cran.scm, gnu/packages/emacs-xyz.scm, gnu/packages/games.scm, gnu/packages/graphics.scm, gnu/packages/haskell-apps.scm, gnu/packages/haskell-check.scm, gnu/packages/idris.scm, gnu/packages/statistics.scm, gnu/packages/wm.scm: Update module references. Co-authored-by: Timothy Sample --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 62f368c139..779a972520 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) -- cgit v1.2.3 From aea33b475b043a24ba1c2d9adbd64119cc142745 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 2 Sep 2019 14:38:44 +0200 Subject: gnu: r-iranges: Update to 2.18.2. * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.18.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 779a972520..02b2cd17e5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7378,13 +7378,13 @@ 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) -- cgit v1.2.3 From e5bc6fce19f848ff8a983a008c35f6d6dc1cd01e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 2 Sep 2019 14:38:48 +0200 Subject: gnu: r-annotationdbi: Update to 1.46.1. * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.46.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 02b2cd17e5..e6a6d082a1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7631,13 +7631,13 @@ 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) -- cgit v1.2.3 From 2c7a32c2acfee352784ba56f8c70f6f38665330d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 2 Sep 2019 14:38:54 +0200 Subject: gnu: r-biomart: Update to 2.40.4. * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e6a6d082a1..02234519d6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7658,13 +7658,13 @@ 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) -- cgit v1.2.3 From 91addfe05c14b6ee10890dfba43847a8a607819a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 2 Sep 2019 14:38:57 +0200 Subject: gnu: r-rtracklayer: Update to 1.44.3. * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 02234519d6..7d6d5e8c48 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7883,13 +7883,13 @@ 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 -- cgit v1.2.3 From 32fcd898f0e73b34dd8f11af952b87707e461f7a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 2 Sep 2019 14:39:11 +0200 Subject: gnu: r-seurat: Update to 3.1.0. * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.0. [propagated-inputs]: Add r-leiden, r-rcppannoy, and r-uwot. --- gnu/packages/bioinformatics.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7d6d5e8c48..2c6648b294 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9457,13 +9457,13 @@ 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 @@ -9480,6 +9480,7 @@ 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) @@ -9490,6 +9491,7 @@ 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) @@ -9500,7 +9502,8 @@ 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 -- cgit v1.2.3 From e107ccea8421cd9b74589b73c15127fc812c3a33 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 2 Sep 2019 14:39:56 +0200 Subject: gnu: r-ldblock: Update to 1.14.2. * gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.14.2. [propagated-inputs]: Remove r-erma; add r-ensdb-hsapiens-v75, r-ensembldb, and r-httr. --- gnu/packages/bioinformatics.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2c6648b294..f5901703ce 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10190,22 +10190,24 @@ 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) -- cgit v1.2.3 From 79c6d8781b1e3d09e1e1555675c144d821487535 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 5 Sep 2019 12:03:38 +0200 Subject: gnu: bwa-meth: Capture one more reference to "bwa". Reported by: Alexander.Blume * gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Capture invocation of "bwa index" to retain reference to "bwa" package. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f5901703ce..f976cad22f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1767,8 +1767,8 @@ 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))))) -- cgit v1.2.3 From 5f9fe21d49fb976e63c93e981abe9304a7bbfcdc Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Thu, 5 Sep 2019 18:26:30 +0200 Subject: gnu: umi-tools: Remove python-setuptools as an input. As this is provided by the build system. * gnu/packages/bioinformatics.scm (umi-tools)[inputs,native-inputs]: Remove python-setuptools. --- gnu/packages/bioinformatics.scm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f976cad22f..2ff5f2c948 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14673,16 +14673,14 @@ 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 -- cgit v1.2.3 From 067ea2989fce98f3f3f115534e2e685cfc681039 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Thu, 5 Sep 2019 18:31:25 +0200 Subject: gnu: python-pyfaidx: Remove python-setuptools as an input. As this is provided by the build system, and I'm assuming that it's not necessary to have it as a propagated input. * gnu/packages/bioinformatics.scm (python-pyfaidx)[propagated-inputs]: Remove python-setuptools. --- gnu/packages/bioinformatics.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2ff5f2c948..9e8d036623 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13433,8 +13433,7 @@ 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 -- cgit v1.2.3 From f480133c4eff49c8f25c951db7d3871aee99d80f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 5 Sep 2019 13:16:06 +0200 Subject: gnu: libbigwig: Update to 0.4.4. * gnu/packages/bioinformatics.scm (libbigwig): Update to 0.4.4. --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9e8d036623..f98f10a2c3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2353,16 +2353,16 @@ 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" -- cgit v1.2.3 From 8205534569cb2a09d53b7c925a349cd7f4e3599d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 6 Sep 2019 15:00:16 +0200 Subject: gnu: Add samblaster. * gnu/packages/bioinformatics.scm (samblaster): New variable. --- gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f98f10a2c3..cf2dc57fa7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15232,3 +15232,37 @@ 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))) -- cgit v1.2.3