gnu: wfmash: Enable test suite.
* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Don't disable tests. Add custom 'check phase based on upstream's own CI tests. [native-inputs]: Add samtools.master
Efraim Flashner
parent
1ca9d9e194
commit
8f3dc994bb
|
|
@ -16154,13 +16154,120 @@ language.")
|
|||
(("!__x86_64__") "0"))))))
|
||||
(build-system cmake-build-system)
|
||||
(arguments
|
||||
(list #:tests? #f)) ; no tests
|
||||
(list
|
||||
#: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 (string-append "../wfmash-v" #$version "/data")
|
||||
"data")
|
||||
(and
|
||||
;; This test takes 60 minutes on riscv64-linux.
|
||||
#$@(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"
|
||||
"data/reads.255bps.fa.gz"
|
||||
"-X" "-w" "16")))
|
||||
(invoke "head" "reads.255bps.paf"))))))))))
|
||||
(inputs
|
||||
(list atomic-queue
|
||||
gsl
|
||||
htslib
|
||||
jemalloc
|
||||
zlib))
|
||||
(native-inputs
|
||||
(list samtools))
|
||||
(synopsis "Base-accurate DNA sequence aligner")
|
||||
(description "@code{wfmash} is a DNA sequence read mapper based on mash
|
||||
distances and the wavefront alignment algorithm. It is a fork of MashMap that
|
||||
|
|
|
|||
Reference in New Issue