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author | Arun Isaac | 2022-04-01 15:22:10 +0530 |
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committer | Arun Isaac | 2022-04-01 15:22:10 +0530 |
commit | 54a2df5f391c4bd367a4a7475a04297e907c137b (patch) | |
tree | 98b567180f670ce15477c3114901c478ec5eeef7 /gn/packages/riscv.scm | |
parent | c2e4d927aadb9c64abe0e7a800c5286e9a3a1463 (diff) | |
download | guix-bioinformatics-54a2df5f391c4bd367a4a7475a04297e907c137b.tar.gz |
gn: wfmash: Remove package.
wfmash has been upstreamed.
* gn/packages/riscv.scm (wfmash): Delete variable.
Diffstat (limited to 'gn/packages/riscv.scm')
-rw-r--r-- | gn/packages/riscv.scm | 169 |
1 files changed, 3 insertions, 166 deletions
diff --git a/gn/packages/riscv.scm b/gn/packages/riscv.scm index 4c40429..9e63665 100644 --- a/gn/packages/riscv.scm +++ b/gn/packages/riscv.scm @@ -10,19 +10,11 @@ ;;; (define-module (gn packages riscv) - #:use-module (guix utils) - #:use-module (guix packages) - #:use-module (guix git-download) - #:use-module (guix build-system gnu) - #: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)) + #:use-module (guix git-download) + #:use-module (guix packages) + #:use-module (guix build-system gnu)) ;; Static hello, for testing @@ -48,158 +40,3 @@ (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)))) |