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-rw-r--r--gn/packages/riscv.scm226
1 files changed, 135 insertions, 91 deletions
diff --git a/gn/packages/riscv.scm b/gn/packages/riscv.scm
index 2e6da2c..90de616 100644
--- a/gn/packages/riscv.scm
+++ b/gn/packages/riscv.scm
@@ -10,95 +10,53 @@
;;;
(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 utils)
+ #:use-module (guix packages)
#:use-module (guix git-download)
+ #:use-module (guix build-system cmake)
#:use-module ((guix licenses) #:prefix license:)
- #:use-module (guix packages)
- #:use-module (guix utils))
+ #: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))
-(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)))
+;; 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 "50a68f0d8c372e720d73e7fc9d90a0d0a4e54ef8")
- (package-revision "25"))
+ (commit "81b8292479648058c6986da808afba0eadcce8d0")
+ (package-revision "26"))
(package
(name "wfmash")
- (version (string-append version "+" (string-take commit 7) "-" package-revision))
+ (version (git-version version package-revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ekg/wfmash.git")
- (commit commit)
- (recursive? #f)))
+ (commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
- "1xf742sxn7xvrcmn67zk9rv8zxl9nb9f72hbw8khdlz1qj3n00vp"))
+ "0nfmbnmlk2ji5f651dkv0jl1h3d1lp2npldwhdiyylp96z3yz8zb"))
(modules '((guix build utils)))
(snippet '(begin
(delete-file-recursively "src/common/atomic_queue")
@@ -107,34 +65,118 @@ ultra-low latency applications.")
"<atomic_queue/atomic_queue.h>"))))))
(build-system cmake-build-system)
(arguments
- `(#:configure-flags '("-DBUILD_SHARED_LIBS=OFF")
- #:phases
- (modify-phases
- %standard-phases
+ `(#: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")
+ (substitute* (find-files "." "CMakeLists\\.txt")
+ (("-mcx16") "")
(("-march=native") ""))
(substitute* "src/common/dset64.hpp"
- (("#error \"wfmash can only be built on an x86_64 machine \\(64-bit Intel/AMD\\)\"")
- ""))))
+ (("__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)))
- #t))
- (delete 'check))
+ (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
@@ -142,6 +184,8 @@ ultra-low latency applications.")
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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-01 14:36:12 +0000