blob: 90de616699952788a9f5afad0a2101383a88ae60 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
|
;;;
;;; 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 bioinformatics)
#:use-module (gnu packages cpp)
#:use-module (gnu packages compression)
#:use-module (gnu packages jemalloc)
#:use-module (gnu packages maths))
;; 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))))
|
