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-rw-r--r--gn/packages/bioinformatics.scm77
1 files changed, 77 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 8bb4e80..b2ff1ed 100644
--- a/gn/packages/bioinformatics.scm
+++ b/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