diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/riscv.scm | 153 |
1 files changed, 153 insertions, 0 deletions
diff --git a/gn/packages/riscv.scm b/gn/packages/riscv.scm new file mode 100644 index 0000000..2e6da2c --- /dev/null +++ b/gn/packages/riscv.scm @@ -0,0 +1,153 @@ +;;; +;;; Commentary: +;;; +;;; This module is a temporary staging ground for Guix packages ported +;;; to RISC-V. They should be contributed upstream at the earliest. +;;; + +;;; +;;; Code: +;;; + +(define-module (gn packages riscv) + #:use-module (gnu packages autotools) + #:use-module ((gnu packages bioinformatics) #:prefix guix:) + #:use-module (gnu packages compression) + #:use-module (gnu packages jemalloc) + #:use-module ((gnu packages maths) #:prefix guix:) + #:use-module (guix build-system cmake) + #:use-module (guix build-system gnu) + #:use-module (guix git-download) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix utils)) + +(define-public htslib + (package + (inherit guix:htslib) + (name "htslib") + (inputs + `(("bzip2" ,bzip2) + ("xz" ,xz) + ,@(package-inputs guix:htslib))))) + +(define-public gsl + (package + (inherit guix:gsl) + (name "gsl") + (arguments + (substitute-keyword-arguments (package-arguments guix:gsl) + ((#:configure-flags _) `(list)) + ((#:phases phases '%standard-phases) + `(modify-phases ,phases + (add-after 'unpack 'force-bootstrap + (lambda _ + (delete-file "configure"))))))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))))) + +(define-public atomic-queue + (package + (name "atomic-queue") + (version "1.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/max0x7ba/atomic_queue") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ssff73wlvrsk2nma99dmvm0ijyzfr54jk37kxgpb694r7ajc90l")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (copy-recursively "include/atomic_queue" + (string-append (assoc-ref outputs "out") + "/include/atomic_queue"))))))) + (home-page "https://github.com/max0x7ba/atomic_queue") + (synopsis "C++ lockless queue") + (description "@code{atomic-queue} provides C++14 +multiple-producer-multiple-consumer lockless queues based on a circular buffer +with std::atomic. The maximum queue size must be set at compile time. And, +there are no OS-blocking push/pop functions, thus making it suitable for +ultra-low latency applications.") + (license license:expat))) + +(define-public wfmash + (let ((version "0.7.0") + (commit "50a68f0d8c372e720d73e7fc9d90a0d0a4e54ef8") + (package-revision "25")) + (package + (name "wfmash") + (version (string-append version "+" (string-take commit 7) "-" package-revision)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/wfmash.git") + (commit commit) + (recursive? #f))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1xf742sxn7xvrcmn67zk9rv8zxl9nb9f72hbw8khdlz1qj3n00vp")) + (modules '((guix build utils))) + (snippet '(begin + (delete-file-recursively "src/common/atomic_queue") + (substitute* "src/align/include/computeAlignments.hpp" + (("\"common/atomic_queue/atomic_queue.h\"") + "<atomic_queue/atomic_queue.h>")))))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags '("-DBUILD_SHARED_LIBS=OFF") + #:phases + (modify-phases + %standard-phases + (add-after 'unpack 'remove-x86-specific-compile-flags + (lambda _ + (substitute* (list "CMakeLists.txt" + "src/common/wflign/CMakeLists.txt" + "src/common/wflign/deps/WFAv2/CMakeLists.txt" + "src/common/wflign/deps/wflambdav2/CMakeLists.txt") + (("-mcx16") "")) + (substitute* (list "CMakeLists.txt" + "src/common/wflign/CMakeLists.txt" + "src/common/wflign/deps/WFAv2/CMakeLists.txt" + "src/common/wflign/deps/wflambdav2/CMakeLists.txt") + (("-march=native") "")) + (substitute* "src/common/dset64.hpp" + (("#error \"wfmash can only be built on an x86_64 machine \\(64-bit Intel/AMD\\)\"") + "")))) + ;; This stashes our build version in the executable + (add-after 'unpack 'set-version + (lambda _ + (mkdir "include") + (with-output-to-file "include/wfmash_git_version.hpp" + (lambda () + (format #t "#define WFMASH_GIT_VERSION \"~a\"~%" version))) + #t)) + (delete 'check)) + #:make-flags (list (string-append "CC=" ,(cc-for-target)) + (string-append "CXX=" ,(cxx-for-target))))) + (inputs (list atomic-queue + gsl + htslib + jemalloc + zlib)) + (synopsis "base-accurate DNA sequence alignments using WFA and mashmap2") + (description "wfmash is a fork of MashMap that implements +base-level alignment using the wavefront alignment algorithm WFA. It +completes an alignment module in MashMap and extends it to enable +multithreaded operation. A single command-line interface simplfies +usage. The PAF output format is harmonized and made equivalent to that +in minimap2, and has been validated as input to seqwish.") + (home-page "https://github.com/ekg/wfmash") + (license license:expat)))) |