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authorArun Isaac2022-03-14 23:49:45 +0530
committerArun Isaac2022-03-14 23:49:45 +0530
commit8cb170336255fa5a236e74001236a7991eb7c9b7 (patch)
treeab5d9ad76bb58479e034c96e31fb70060a69ae98 /gn/packages
parentf539d5b3ec13f78e1026c409d8e144b96df474e9 (diff)
downloadguix-bioinformatics-8cb170336255fa5a236e74001236a7991eb7c9b7.tar.gz
gn: Add wfmash.
This patch adds a version of wfmash that builds and runs successfully on RISC-V. * gn/packages/riscv.scm: New file.
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/riscv.scm153
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))))