gn: wfmash: Remove package.

wfmash has been upstreamed.

* gn/packages/riscv.scm (wfmash): Delete variable.

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))))