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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 (guix utils)
#:use-module (guix packages)
#:use-module (guix git-download)
#:use-module (guix build-system cmake)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages cpp)
#:use-module (gnu packages compression)
#:use-module (gnu packages jemalloc)
#:use-module (gnu packages maths))
;; Static hello, for testing
(define-public hello-static
(package
(inherit hello)
(name "hello-static")
(arguments
(substitute-keyword-arguments (package-arguments hello)
((#:make-flags _ ''())
`(list "CFLAGS=-static"))))))
;; Improvements to riscv support have been merged since the last release.
(define-public atomic-queue-git
(let ((commit "7d75e9ed0359650224b29cdf6728c5fe0a19fffb") ; 2022-03-11
(revision "1"))
(package
(inherit atomic-queue)
(name "atomic-queue")
(version (git-version "1.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/max0x7ba/atomic_queue")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1dh8x0ikfwk0by5avwfv9gvr9ay6jy13yr66rvgw9wwyxmklz848")))))))
(define-public wfmash
(let ((version "0.7.0")
(commit "81b8292479648058c6986da808afba0eadcce8d0")
(package-revision "26"))
(package
(name "wfmash")
(version (git-version version package-revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ekg/wfmash.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0nfmbnmlk2ji5f651dkv0jl1h3d1lp2npldwhdiyylp96z3yz8zb"))
(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
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'remove-x86-specific-compile-flags
(lambda _
(substitute* (find-files "." "CMakeLists\\.txt")
(("-mcx16") "")
(("-march=native") ""))
(substitute* "src/common/dset64.hpp"
(("__x86_64__" all) (string-append all " && " all)))))
;; 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)))))
(replace 'check
;; Adapted from .github/workflows/test_on_push.yml
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(and
;; This test takes 60 minutes on riscv64-linux.
,@(if (not (target-riscv64?))
`((begin
;; Test with a subset of the LPA dataset (PAF output)
(setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1")
(setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1")
(with-output-to-file "LPA.subset.paf"
(lambda _
(invoke "bin/wfmash"
"../source/data/LPA.subset.fa.gz"
"../source/data/LPA.subset.fa.gz"
"-X" "-n" "10" "-T" "wflign_info.")))
(invoke "head" "LPA.subset.paf")))
'())
;; This test takes about 5 hours on riscv64-linux.
,@(if (not (target-riscv64?))
`((begin
;; Test with a subset of the LPA dataset (SAM output)
(setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1")
(setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1")
(with-output-to-file "LPA.subset.sam"
(lambda _
(invoke "bin/wfmash"
"../source/data/LPA.subset.fa.gz"
"../source/data/LPA.subset.fa.gz"
"-X" "-N" "-a" "-T" "wflign_info.")))
(with-output-to-file "LPA.subset.sam-view"
(lambda _
(invoke "samtools" "view" "LPA.subset.sam" "-bS")))
(with-output-to-file "LPA.subset.bam"
(lambda _
(invoke "samtools" "sort" "LPA.subset.sam-view")))
(invoke "samtools" "index" "LPA.subset.bam")
;; samtools view LPA.subset.bam | head | cut -f 1-9
;(invoke "samtools" "view" "LPA.subset.bam")
;; There should be an easier way to do this with pipes.
(with-output-to-file "LPA.subset.bam-incr1"
(lambda _
(invoke "samtools" "view" "LPA.subset.bam")))
(with-output-to-file "LPA.subset.bam-incr2"
(lambda _
(invoke "head" "LPA.subset.bam-incr1")))
(invoke "cut" "-f" "1-9" "LPA.subset.bam-incr2")))
'())
;; This test takes 60 minutes on riscv64-linux.
,@(if (not (target-riscv64?))
`((begin
;; Test with a subset of the LPA dataset,
;; setting a lower identity threshold (PAF output)
(setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1")
(setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1")
(with-output-to-file "LPA.subset.p90.paf"
(lambda _
(invoke "bin/wfmash"
"../source/data/LPA.subset.fa.gz"
"../source/data/LPA.subset.fa.gz"
"-X" "-p" "90" "-n" "10" "-T" "wflign_info.")))
(invoke "head" "LPA.subset.p90.paf")))
'())
(begin
;; Test aligning short reads (500 bps) to a reference (SAM output)
(setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1")
(setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1")
(with-output-to-file "reads.500bps.sam"
(lambda _
(invoke "bin/wfmash"
"../source/data/reference.fa.gz"
"../source/data/reads.500bps.fa.gz"
"-s" "0.5k" "-N" "-a")))
(with-output-to-file "reads.500bps.sam-view"
(lambda _
(invoke "samtools" "view" "reads.500bps.sam" "-bS")))
(with-output-to-file "reads.500bps.bam"
(lambda _
(invoke "samtools" "sort" "reads.500bps.sam-view")))
(invoke "samtools" "index" "reads.500bps.bam")
(with-output-to-file "reads.500bps.bam-view"
(lambda _
(invoke "samtools" "view" "reads.500bps.bam")))
(invoke "head" "reads.500bps.bam-view"))
(begin
;; Test with few very short reads (255bps) (PAF output)
(setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1")
(setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1")
(with-output-to-file "reads.255bps.paf"
(lambda _
(invoke "bin/wfmash"
"../source/data/reads.255bps.fa.gz"
"../source/data/reads.255bps.fa.gz"
"-X")))
(invoke "head" "reads.255bps.paf")))))))
#:make-flags (list (string-append "CC=" ,(cc-for-target))
(string-append "CXX=" ,(cxx-for-target)))))
(inputs (list atomic-queue
gsl
htslib
jemalloc
zlib))
(native-inputs
(list samtools))
(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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