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gn: Add pirs.

wip-tensorflow
Efraim Flashner 11 months ago
parent
commit
8ad9768e05
Signed by: efraim GPG Key ID: 41AAE7DCCA3D8351
  1. 77
      gn/packages/bioinformatics.scm

77
gn/packages/bioinformatics.scm

@ -21,6 +21,7 @@
#:use-module (gn packages python)
#:use-module (gn packages twint)
#:use-module (gnu packages algebra)
#:use-module (gnu packages autotools)
#:use-module (gnu packages base)
#:use-module (gnu packages bash)
#:use-module (gnu packages bioconductor)
@ -567,6 +568,82 @@ PacBio, and Nanopore reads. In it sampling-based and model-based simulations
are implemented.")
(license license:gpl2))))
(define-public pirs
(let ((commit "bee9b594f4d0e10580aae77ec411cecec4a77219") ; Sept 7, 2017
(revision "1"))
(package
(name "pirs")
(version (git-version "2.0.2" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/galaxy001/pirs")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0pn74h98cqcr5qayp4riss982n4272p35y5dp472cmqpwjjil9cd"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags (list "--enable-pirs-diploid"
;; TODO: Enable after core-updates merge, late 2021.
;,@(if (not (or (target-x86-64?)
; (target-x86-32?)))
; `("--disable-sse2")
; '())
)
#:phases
(modify-phases %standard-phases
(add-before 'bootstrap 'chdir
(lambda _
(chdir "src")))
(add-after 'unpack 'patch-source
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(substitute* "src/configure.ac"
(("ssse2") "sse2"))
(substitute* "src/stator/gcContCvgBias/Makefile"
(("gzstream.o ") "")
(("-lz")"-lgzstream -lz")
(("-static") "")
(("-mtune=generic") ""))
(substitute* "src/pirs/gccMakefile"
(("/usr/local") out)))))
(replace 'check
(lambda* (#:key tests? test-target #:allow-other-keys #:rest args)
(when tests?
(apply (assoc-ref %standard-phases 'check) args)
(with-directory-excursion "stator/gcContCvgBias"
; ((assoc-ref %standard-phases 'check)
; #:test-target "test" args))
(invoke "make" "test")))))
(add-after 'build 'build-more
(lambda* (#:key #:allow-other-keys #:rest args)
(with-directory-excursion "stator/gcContCvgBias"
(apply (assoc-ref %standard-phases 'build) args))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys #:rest args)
(let ((out (assoc-ref outputs "out")))
(apply (assoc-ref %standard-phases 'install) args)
(with-directory-excursion "stator/gcContCvgBias"
;(apply (assoc-ref %standard-phases 'install) args)
(install-file "gc_coverage_bias" (string-append out "/bin")))))))))
(inputs
`(("gnuplot" ,gnuplot)
("perl" ,perl)
("zlib" ,zlib)))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("boost" ,boost)
("gzstream" ,gzstream)
("libtool" ,libtool)))
(home-page "https://github.com/galaxy001/pirs")
(synopsis "Profile based Illumina pair-end Reads Simulator")
(description "@code{pIRS} is a program for simulating paired-end reads
from a reference genome. It is optimized for simulating reads similar to those
generated from the Illumina platform.")
(license license:gpl2))))
;; TODO: Unbundle zlib, bamtools, tclap
(define-public sniffles
(package

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