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;;;
;;; 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))))
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