diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 112 |
1 files changed, 60 insertions, 52 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index af8f322..034daf0 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -3,6 +3,7 @@ (define-module (gn packages bioinformatics) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) + #:use-module (guix gexp) #:use-module (guix utils) #:use-module (guix download) #:use-module (guix git-download) @@ -32,6 +33,7 @@ #:use-module (gnu packages check) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) + #:use-module (gnu packages cpp) #:use-module (gnu packages cran) #:use-module (gnu packages crates-io) #:use-module (gnu packages curl) @@ -1289,64 +1291,70 @@ dictionaries to record a queryable version of the graph.") (description "") (license license:lgpl2.0+)))) ; README just says "lpgl". -;; TODO: Unbundle BBHash, concurrentqueue, parallel-hashmap zstr +;; TODO: Unbundle BBHash, parallel-hashmap, zstr (define-public graphaligner (package - (name "graphaligner") - (version "1.0.10") - (source (origin - (method url-fetch) - (uri (string-append "https://github.com/maickrau/GraphAligner/files/" - "3879798/GraphAligner.tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 "0sk0cfjw44wslmlgplzwcqi0w4862vhf75p4x6syalvyi34pw3ck")))) - (build-system gnu-build-system) - (arguments - `(#:tests? #f ; no tests - #:make-flags '("all") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-source - (lambda* (#:key inputs #:allow-other-keys) - (let ((sdsl (assoc-ref inputs "sdsl-lite"))) - (substitute* "makefile" - (("VERSION .*") (string-append "VERSION = " ,version "\n")))) - #t)) - (delete 'configure) ; no configure phase - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (for-each - (lambda (program) - (install-file program (string-append out "/bin"))) - (find-files "bin" ".")) - (for-each - (lambda (header) - (install-file header (string-append out "/include"))) - (find-files "src" "\\.h(pp)?$"))) - #t))))) - (native-inputs - `(("pkg-config" ,pkg-config) - ("protobuf" ,protobuf "static") - ("sdsl-lite" ,sdsl-lite) - ("sparsehash" ,sparsehash) - ("zlib" ,zlib "static"))) - (inputs - `(("boost" ,boost-static) - ("jemalloc" ,jemalloc) - ("libdivsufsort" ,libdivsufsort) - ("mummer" ,mummer) - ("protobuf" ,protobuf) - ("zlib" ,zlib))) - (home-page "https://github.com/maickrau/GraphAligner") - (synopsis "Seed-and-extend program for aligning genome graphs") - (description "Seed-and-extend program for aligning long error-prone reads to + (name "graphaligner") + (version "1.0.14") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/maickrau/GraphAligner/files/" + "7813545/GraphAligner.tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1y4vwp03fl2ck6bnyn0sc97vgvdb8i0yfzjk5mv5gk0bc7a4f0n1")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ; no tests + #:make-flags + #~(list (string-append "VERSION=" #$version)) + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; no configure phase + (add-after 'unpack 'patch-source + (lambda* (#:key inputs #:allow-other-keys) + (let ((concurrentqueue (assoc-ref inputs "concurrentqueue"))) + (delete-file-recursively "concurrentqueue") + (substitute* "makefile" + (("-Iconcurrentqueue") + (string-append "-I" concurrentqueue "/include/concurrentqueue")) + (("^JEMALLOCFLAGS.*") + "JEMALLOCFLAGS= `pkg-config --libs jemalloc`\n") + ;; No need to build statically. + (("-Wl,-Bstatic") "") + (("-static-libstdc\\+\\+") ""))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (for-each + (lambda (program) + (install-file program (string-append out "/bin"))) + (find-files "bin")) + (for-each + (lambda (header) + (install-file header (string-append out "/include"))) + (find-files "src" "\\.h(pp)?$")))))))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("sparsehash" ,sparsehash))) + (inputs + `(("boost" ,boost) + ("concurrentqueue" ,concurrentqueue) + ("jemalloc" ,jemalloc) + ("libdivsufsort" ,libdivsufsort) + ("mummer" ,mummer) + ("protobuf" ,protobuf) + ("sdsl-lite" ,sdsl-lite) + ("zlib" ,zlib))) + (home-page "https://github.com/maickrau/GraphAligner") + (synopsis "Seed-and-extend program for aligning genome graphs") + (description "Seed-and-extend program for aligning long error-prone reads to genome graphs. For a description of the bitvector alignment extension algorithm, see @url{https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz162/5372677 here}.") - (license license:expat))) + (license license:expat))) (define-public mummer (package |