diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 82 |
1 files changed, 37 insertions, 45 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 07c70fb82c..74a44874ee 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -84,10 +84,10 @@ #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) #:use-module (gnu packages java-compression) + #:use-module (gnu packages javascript) #: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) @@ -105,6 +105,7 @@ #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages python-compression) + #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages readline) @@ -983,16 +984,17 @@ e.g. microbiome samples, genomes, metagenomes.") (version "1.7.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/bioperl/bioperl-live/" - "archive/release-" - (string-map (lambda (c) - (if (char=? c #\.) - #\- c)) version) - ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/bioperl/bioperl-live") + (commit (string-append "release-" + (string-map (lambda (c) + (if (char=? c #\.) + #\- c)) version))))) + (file-name (git-file-name name version)) (sha256 (base32 - "12phgpxwgkqflkwfb9dcqg7a31dpjlfhar8wcgv0aj5ln4akfz06")))) + "0wl8yvzcls59pwwk6m8ahy87pwg6nnibzy5cldbvmcwg2x2w7783")))) (build-system perl-build-system) (arguments `(#:phases @@ -11271,7 +11273,8 @@ models. TADbit is complemented by TADkit for visualizing 3D models.") ("tcsh" ,tcsh) ("perl" ,perl) ("libpng" ,libpng) - ("mariadb" ,mariadb) + ("mariadb" ,mariadb "lib") + ("mariadb-dev" ,mariadb "dev") ("openssl" ,openssl))) (home-page "http://genome.cse.ucsc.edu/index.html") (synopsis "Assorted bioinformatics utilities") @@ -11571,35 +11574,6 @@ provide this functionality without the necessity of drawing in a heavy-weight dependency like SeqAn.") (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt")))) -(define-public libdivsufsort - (package - (name "libdivsufsort") - (version "2.0.1") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/y-256/libdivsufsort.git") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2")))) - (build-system cmake-build-system) - (arguments - '(#:tests? #f ; there are no tests - #:configure-flags - ;; Needed for rapmap and sailfish. - '("-DBUILD_DIVSUFSORT64=ON"))) - (home-page "https://github.com/y-256/libdivsufsort") - (synopsis "Lightweight suffix-sorting library") - (description "libdivsufsort is a software library that implements a -lightweight suffix array construction algorithm. This library provides a -simple and an efficient C API to construct a suffix array and a -Burrows-Wheeler transformed string from a given string over a constant-size -alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1) -bytes of memory space, where n is the length of the string.") - (license license:expat))) - (define-public sailfish (package (name "sailfish") @@ -13890,7 +13864,7 @@ datasets.") (define-public ngless (package (name "ngless") - (version "0.9.1") + (version "1.0.1") (source (origin (method git-fetch) @@ -13900,7 +13874,7 @@ datasets.") (file-name (git-file-name name version)) (sha256 (base32 - "0mc2gi7h4lx74zylvyp76mvc0w6706j858ii9vlgzqsw6acpr117")))) + "06ygv8q2zjqsnrid1302yrlhhvb8ik48nq6n0higk3i1mdc8r0dg")))) (build-system haskell-build-system) (arguments `(#:haddock? #f ; The haddock phase fails with: NGLess/CmdArgs.hs:20:1: @@ -13908,7 +13882,24 @@ datasets.") ; import Options.Applicative #:phases (modify-phases %standard-phases - (add-after 'unpack 'create-cabal-file + (add-after 'unpack 'create-Versions.hs + (lambda _ + (substitute* "Makefile" + (("BWA_VERSION = .*") + (string-append "BWA_VERSION = " + ,(package-version bwa) "\n")) + (("SAM_VERSION = .*") + (string-append "SAM_VERSION = " + ,(package-version samtools) "\n")) + (("PRODIGAL_VERSION = .*") + (string-append "PRODIGAL_VERSION = " + ,(package-version prodigal) "\n")) + (("MINIMAP2_VERSION = .*") + (string-append "MINIMAP2_VERSION = " + ,(package-version minimap2) "\n"))) + (invoke "make" "NGLess/Dependencies/Versions.hs") + #t)) + (add-after 'create-Versions.hs 'create-cabal-file (lambda _ (invoke "hpack") #t)) ;; These tools are expected to be installed alongside ngless. (add-after 'install 'link-tools @@ -13937,15 +13928,15 @@ datasets.") ("ghc-async" ,ghc-async) ("ghc-atomic-write" ,ghc-atomic-write) ("ghc-bytestring-lexing" ,ghc-bytestring-lexing) - ("ghc-chart" ,ghc-chart) - ("ghc-chart-cairo" ,ghc-chart-cairo) ("ghc-conduit" ,ghc-conduit) ("ghc-conduit-algorithms" ,ghc-conduit-algorithms) - ("ghc-conduit-combinators" ,ghc-conduit-combinators) ("ghc-conduit-extra" ,ghc-conduit-extra) ("ghc-configurator" ,ghc-configurator) ("ghc-convertible" ,ghc-convertible) ("ghc-data-default" ,ghc-data-default) + ("ghc-diagrams-core" ,ghc-diagrams-core) + ("ghc-diagrams-lib" ,ghc-diagrams-lib) + ("ghc-diagrams-svg" ,ghc-diagrams-svg) ("ghc-double-conversion" ,ghc-double-conversion) ("ghc-edit-distance" ,ghc-edit-distance) ("ghc-either" ,ghc-either) @@ -13966,6 +13957,7 @@ datasets.") ("ghc-safeio" ,ghc-safeio) ("ghc-strict" ,ghc-strict) ("ghc-tar" ,ghc-tar) + ("ghc-tar-conduit" ,ghc-tar-conduit) ("ghc-unliftio" ,ghc-unliftio) ("ghc-unliftio-core" ,ghc-unliftio-core) ("ghc-vector" ,ghc-vector) |