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-rw-r--r--gnu/packages/bioinformatics.scm145
1 files changed, 31 insertions, 114 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d167a11ba1..16f8bfd462 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -22991,18 +22991,15 @@ based on the pairwise alignment of hidden Markov models (HMMs).")
(define-public wfmash
(package
(name "wfmash")
- (version "0.12.5")
+ (version "0.21.0")
(source
(origin
- ;; There are no release tarballs after version 0.10.5.
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/waveygang/wfmash")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
+ (method url-fetch)
+ (uri (string-append "https://github.com/waveygang/wfmash/releases/download/v"
+ version "/wfmash-v" version ".tar.gz"))
(sha256
(base32
- "1qh2chnwp7nqgp88afc4xzdkd21vh6cfqq73siqw7vc0qinqadm6"))
+ "0v9giqrqxl9kkcrs6zrfj1y07j6p9r8d82kkwigvndlg1708457w"))
(snippet
#~(begin
(use-modules (guix build utils))
@@ -23017,116 +23014,36 @@ based on the pairwise alignment of hidden Markov models (HMMs).")
(build-system cmake-build-system)
(arguments
(list
- #:configure-flags
- #~(list "-DWFA_PNG_AND_TSV=ON")
- #:phases
- #~(modify-phases %standard-phases
- (replace 'check
- ;; Adapted from .github/workflows/test_on_push.yml
- (lambda* (#:key tests? inputs #:allow-other-keys)
- (when tests?
- (let ((samtools (search-input-file inputs "/bin/samtools")))
- ;; This is the easiest way to access the data
- ;; needed for the test suite.
- (symlink "../source/data" "data")
- (and
- ;; This test takes 60 minutes on riscv64-linux.
- #$@(if (not (target-riscv64?))
- #~((begin
- ;; Test with a subset of the LPA dataset (PAF output)
- (setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1")
- (setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1")
- (with-output-to-file "LPA.subset.paf"
- (lambda _
- (invoke "bin/wfmash"
- "data/LPA.subset.fa.gz"
- "data/LPA.subset.fa.gz"
- "-X" "-n" "10" "-T" "wflign_info."
- "-u" "./")))
- (invoke "head" "LPA.subset.paf")))
- #~())
- ;; This test takes about 5 hours on riscv64-linux.
- #$@(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"
- "data/LPA.subset.fa.gz"
- "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"
- "data/LPA.subset.fa.gz"
- "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"
- "data/reference.fa.gz"
- "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"
- "data/reads.255bps.fa.gz"
- "-w" "16" "-s" "100" "-L")))
- (invoke "head" "reads.255bps.paf"))))))))))
+ #:configure-flags
+ #~(list "-DWFA_PNG_AND_TSV=ON")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'fix-cmakelists
+ (lambda _
+ (substitute* "CMakeLists.txt"
+ ;; Remove broken configure of CTestCustom.cmake.
+ (("^configure_file[^\n]*") "")
+ ;; Do not hard-code wfmash executable.
+ (("\\./build/bin/wfmash") "wfmash"))))
+ (add-before 'check 'build-check-prerequisites
+ (lambda _
+ (let ((wfa2-lib #$(string-append "../wfmash-v"
+ version
+ "/src/common/wflign/deps/WFA2-lib")))
+ (substitute* (string-append wfa2-lib "/Makefile")
+ ;; Remove architecture-specific flags.
+ (("-march=x86-64-v3") ""))
+ (substitute* (string-append wfa2-lib "/tests/wfa.utest.sh")
+ ;; Fix time command.
+ (("\\\\time -v") "time"))
+ ;; Build wfa2-lib.
+ (invoke "make" "-C" wfa2-lib
+ #$(string-append "CC=" (cc-for-target)))))))))
(inputs
(list atomic-queue
gsl
htslib
- jemalloc
+ libdeflate
zlib))
(native-inputs
(list pkg-config
generated by cgit