diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 77 |
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 |