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gnu: wfmash: Update to 0.21.0.
* gnu/packages/bioinformatics.scm (wfmash): Update to 0.21.0. [source]: Use url-fetch. [arguments]: Do not replace standard check phase. Add fix-cmakelists and build-check-prerequisites phases. [inputs]: Remove jemalloc. Add libdeflate. Change-Id: I664178e9fac7320b9d6e3190e8a3779b2bce2c6b
This commit is contained in:
Arun Isaac
parent
b8f8699a1f
commit
789300000c
1 changed files with 31 additions and 114 deletions
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@ -22991,18 +22991,15 @@ based on the pairwise alignment of hidden Markov models (HMMs).")
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(define-public wfmash
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(define-public wfmash
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(package
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(package
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(name "wfmash")
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(name "wfmash")
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(version "0.12.5")
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(version "0.21.0")
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(source
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(source
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(origin
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(origin
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;; There are no release tarballs after version 0.10.5.
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(method url-fetch)
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(method git-fetch)
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(uri (string-append "https://github.com/waveygang/wfmash/releases/download/v"
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(uri (git-reference
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version "/wfmash-v" version ".tar.gz"))
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(url "https://github.com/waveygang/wfmash")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(sha256
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(base32
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(base32
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"1qh2chnwp7nqgp88afc4xzdkd21vh6cfqq73siqw7vc0qinqadm6"))
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"0v9giqrqxl9kkcrs6zrfj1y07j6p9r8d82kkwigvndlg1708457w"))
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(snippet
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(snippet
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#~(begin
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#~(begin
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(use-modules (guix build utils))
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(use-modules (guix build utils))
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@ -23017,116 +23014,36 @@ based on the pairwise alignment of hidden Markov models (HMMs).")
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(build-system cmake-build-system)
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(build-system cmake-build-system)
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(arguments
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(arguments
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(list
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(list
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#:configure-flags
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#:configure-flags
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#~(list "-DWFA_PNG_AND_TSV=ON")
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#~(list "-DWFA_PNG_AND_TSV=ON")
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#:phases
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#:phases
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#~(modify-phases %standard-phases
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#~(modify-phases %standard-phases
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(replace 'check
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(add-after 'unpack 'fix-cmakelists
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;; Adapted from .github/workflows/test_on_push.yml
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(lambda _
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(lambda* (#:key tests? inputs #:allow-other-keys)
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(substitute* "CMakeLists.txt"
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(when tests?
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;; Remove broken configure of CTestCustom.cmake.
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(let ((samtools (search-input-file inputs "/bin/samtools")))
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(("^configure_file[^\n]*") "")
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;; This is the easiest way to access the data
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;; Do not hard-code wfmash executable.
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;; needed for the test suite.
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(("\\./build/bin/wfmash") "wfmash"))))
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(symlink "../source/data" "data")
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(add-before 'check 'build-check-prerequisites
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(and
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(lambda _
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;; This test takes 60 minutes on riscv64-linux.
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(let ((wfa2-lib #$(string-append "../wfmash-v"
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#$@(if (not (target-riscv64?))
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version
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#~((begin
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"/src/common/wflign/deps/WFA2-lib")))
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;; Test with a subset of the LPA dataset (PAF output)
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(substitute* (string-append wfa2-lib "/Makefile")
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(setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1")
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;; Remove architecture-specific flags.
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(setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1")
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(("-march=x86-64-v3") ""))
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(with-output-to-file "LPA.subset.paf"
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(substitute* (string-append wfa2-lib "/tests/wfa.utest.sh")
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(lambda _
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;; Fix time command.
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(invoke "bin/wfmash"
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(("\\\\time -v") "time"))
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"data/LPA.subset.fa.gz"
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;; Build wfa2-lib.
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"data/LPA.subset.fa.gz"
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(invoke "make" "-C" wfa2-lib
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"-X" "-n" "10" "-T" "wflign_info."
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#$(string-append "CC=" (cc-for-target)))))))))
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"-u" "./")))
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(invoke "head" "LPA.subset.paf")))
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#~())
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;; This test takes about 5 hours on riscv64-linux.
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#$@(if (not (target-riscv64?))
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#~((begin
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;; Test with a subset of the LPA dataset (SAM output)
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(setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1")
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(setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1")
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(with-output-to-file "LPA.subset.sam"
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(lambda _
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(invoke "bin/wfmash"
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"data/LPA.subset.fa.gz"
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"data/LPA.subset.fa.gz"
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"-X" "-N" "-a" "-T" "wflign_info.")))
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(with-output-to-file "LPA.subset.sam-view"
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(lambda _
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(invoke samtools "view" "LPA.subset.sam" "-bS")))
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(with-output-to-file "LPA.subset.bam"
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(lambda _
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(invoke samtools "sort" "LPA.subset.sam-view")))
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(invoke samtools "index" "LPA.subset.bam")
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;; samtools view LPA.subset.bam | head | cut -f 1-9
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;(invoke samtools "view" "LPA.subset.bam")
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;; There should be an easier way to do this with pipes.
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(with-output-to-file "LPA.subset.bam-incr1"
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(lambda _
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(invoke samtools "view" "LPA.subset.bam")))
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(with-output-to-file "LPA.subset.bam-incr2"
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(lambda _
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(invoke "head" "LPA.subset.bam-incr1")))
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(invoke "cut" "-f" "1-9" "LPA.subset.bam-incr2")))
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#~())
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;; This test takes 60 minutes on riscv64-linux.
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#$@(if (not (target-riscv64?))
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#~((begin
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;; Test with a subset of the LPA dataset,
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;; setting a lower identity threshold (PAF output)
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(setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1")
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(setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1")
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(with-output-to-file "LPA.subset.p90.paf"
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(lambda _
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(invoke "bin/wfmash"
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"data/LPA.subset.fa.gz"
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"data/LPA.subset.fa.gz"
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"-X" "-p" "90" "-n" "10"
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"-T" "wflign_info.")))
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(invoke "head" "LPA.subset.p90.paf")))
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#~())
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(begin
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;; Test aligning short reads (500 bps) to a reference (SAM output)
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(setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1")
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(setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1")
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(with-output-to-file "reads.500bps.sam"
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(lambda _
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(invoke "bin/wfmash"
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"data/reference.fa.gz"
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"data/reads.500bps.fa.gz"
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"-s" "0.5k" "-N" "-a")))
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(with-output-to-file "reads.500bps.sam-view"
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(lambda _
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(invoke samtools "view" "reads.500bps.sam" "-bS")))
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(with-output-to-file "reads.500bps.bam"
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(lambda _
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(invoke samtools "sort" "reads.500bps.sam-view")))
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(invoke samtools "index" "reads.500bps.bam")
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(with-output-to-file "reads.500bps.bam-view"
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(lambda _
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(invoke samtools "view" "reads.500bps.bam")))
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(invoke "head" "reads.500bps.bam-view"))
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(begin
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;; Test with few very short reads (255bps) (PAF output)
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(setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1")
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(setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1")
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(with-output-to-file "reads.255bps.paf"
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(lambda _
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(invoke "bin/wfmash"
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"data/reads.255bps.fa.gz"
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"-w" "16" "-s" "100" "-L")))
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(invoke "head" "reads.255bps.paf"))))))))))
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(inputs
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(inputs
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(list atomic-queue
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(list atomic-queue
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gsl
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gsl
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htslib
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htslib
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jemalloc
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libdeflate
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zlib))
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zlib))
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(native-inputs
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(native-inputs
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(list pkg-config
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(list pkg-config
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