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-rw-r--r--gn/packages/bioinformatics.scm212
1 files changed, 212 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 8f79cdb..23d1524 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -19,10 +19,12 @@
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages cran)
+ #:use-module (gnu packages datastructures)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gcc)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages maths)
+ #:use-module (gnu packages mpi)
#:use-module (gnu packages perl)
#:use-module (gnu packages python)
#:use-module (gnu packages python-xyz)
@@ -847,3 +849,213 @@ recombinant inbred population. A power calculator such as this is needed as all
grants require a calculation of the applications power to detect the effect of
interest, and this app can provide values and figures for applicants to use.")
(license license:gpl3))))
+
+(define-public seqwish
+ (package
+ (name "seqwish")
+ (version "0.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/seqwish.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1gp72cmi13hbkmwwhgckmxkbx8w644jc5l6dvvvxdbl6sk8xsi5r"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'build
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((sdsl-lite (assoc-ref inputs "sdsl-lite"))
+ (bsort (assoc-ref inputs "bsort"))
+ (mmap_allocator (assoc-ref inputs "mmap-allocator"))
+ (tayweeargs (assoc-ref inputs "tayweeargs-source"))
+ (gzipreader (assoc-ref inputs "gzipreader-source"))
+ (mmmultimap (assoc-ref inputs "mmmultimap-source"))
+ (iitii (assoc-ref inputs "iitii-source"))
+ (ips4o (assoc-ref inputs "ips4o-source")))
+ (apply invoke "g++" "-o" "seqwish"
+ "-O3" "-g" "-std=c++14" "-fopenmp"
+ "-latomic" "-lz"
+ (string-append "-I" sdsl-lite "/include")
+ (string-append "-I" sdsl-lite "/include/sdsl")
+ (string-append "-I" bsort "/include")
+ (string-append "-I" tayweeargs)
+ (string-append "-I" gzipreader)
+ (string-append "-I" mmmultimap "/src")
+ (string-append "-I" iitii "/src")
+ (string-append "-I" mmap_allocator "/include")
+ (string-append "-I" ips4o)
+ (append
+ (find-files "src" ".")
+ (list
+ (string-append sdsl-lite "/lib/libsdsl.a")
+ (string-append sdsl-lite "/lib/libdivsufsort.a")
+ (string-append sdsl-lite "/lib/libdivsufsort64.a")
+ (string-append mmap_allocator "/lib/libmmap_allocator.a")
+ (string-append bsort "/lib/libbsort.a")))))))
+ (replace 'check
+ (lambda _
+ ;; Add seqwish to the PATH for the tests.
+ (setenv "PATH" (string-append (getcwd) ":" (getenv "PATH")))
+ (with-directory-excursion "test"
+ (invoke "make"))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (install-file "seqwish" (string-append out "/bin")))
+ #t)))))
+ (inputs
+ `(("bsort" ,ekg-bsort)
+ ("mmap-allocator" ,ekg-mmap-allocator)
+ ("openmpi" ,openmpi)
+ ("sdsl-lite" ,sdsl-lite-gn)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("prove" ,perl)
+ ("tayweeargs-source" ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/Taywee/args.git")
+ (commit "3de44ec671db452cc0c4ef86399b108939768abb")))
+ (file-name "tayweeargs-source-for-seqwish")
+ (sha256
+ (base32
+ "1v8kq1gvl5waysrfp0s58881rx39mnf3ifdsl6pb3y3c4zaki2xh"))))
+ ("gzipreader-source" ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/gatoravi/gzip_reader.git")
+ (commit "0ef26c0399e926087f9d6c4a56067a7bf1fc4f5e")))
+ (file-name "gzipreader-source-for-seqwish")
+ (sha256
+ (base32
+ "1wy84ksx900840c06w0f1mgzvr7zsfsgxq1b0jdjh8qka26z1r17"))))
+ ("mmmultimap-source" ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/mmmultimap.git")
+ (commit "88c734c36563048b0f3acc04dd8856f19e02b75f")))
+ (file-name "mmmultimap-source-for-seqwish")
+ (sha256
+ (base32
+ "06mnf3bd32s3ngxkl573ylg2qsvlw80r1ksdwamx3fzxa1a5yls0"))))
+ ("iitii-source" ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/iitii.git")
+ (commit "85209e07a3ee403fb6557387a7f897cd76be4406")))
+ (file-name "iitii-source-for-seqwish")
+ (sha256
+ (base32
+ "0sszvffkswf89nkbjmjg3wjwqvy2w0d3wgy3ngy33ma4sy4s025s"))))
+ ("ips4o-source" ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/SaschaWitt/ips4o.git")
+ (commit "bff3ccf0bf349497f2bb10f825d160b792236367")))
+ (file-name "ips4o-source-for-seqwish")
+ (sha256
+ (base32
+ "0yjfvrkiwgmy5cn0a7b9j8jwc3zp0l8j4dl5n0jgz68pdnhlp96h"))))))
+ (home-page "https://github.com/ekg/seqwish")
+ (synopsis "Alignment to variation graph inducer")
+ (description "Seqwish implements a lossless conversion from pairwise
+alignments between sequences to a variation graph encoding the sequences and
+their alignments. As input we typically take all-versus-all alignments, but the
+exact structure of the alignment set may be defined in an application specific
+way. This algorithm uses a series of disk-backed sorts and passes over the
+alignment and sequence inputs to allow the graph to be constructed from very
+large inputs that are commonly encountered when working with large numbers of
+noisy input sequences. Memory usage during construction and traversal is
+limited by the use of sorted disk-backed arrays and succinct rank/select
+dictionaries to record a queryable version of the graph.")
+ (license license:expat)))
+
+(define sdsl-lite-gn
+ (package
+ (inherit sdsl-lite)
+ (name "sdsl-lite-gn")
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (add-after 'install 'install-libdivsufsort
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (install-file "lib/libdivsufsort.a" (string-append out "/lib"))
+ (install-file "lib/libdivsufsort64.a" (string-append out "/lib"))
+ #t))))))))
+
+(define ekg-bsort
+ (let ((commit "c3ab0d3308424030e0a000645a26d2c10a59a124")
+ (revision "1"))
+ (package
+ (name "bsort")
+ (version (git-version "0.0.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/bsort.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0dgpflzcp3vdhbjwbjw347czi86gyk73hxcwjdqnaqh5vg61bdb6"))))
+ (build-system cmake-build-system)
+ (arguments
+ '(#:tests? #f ; no test target
+ #:out-of-source? #f
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (install-file "bin/bsort" (string-append out "/bin"))
+ (install-file "src/bsort.hpp" (string-append out "/include"))
+ (install-file "lib/libbsort.a" (string-append out "/lib")))
+ #t)))))
+ (home-page "")
+ (synopsis "")
+ (description "")
+ (license license:gpl2))))
+
+(define ekg-mmap-allocator
+ (let ((commit "ed61daf094de1c2e1adbe8306287ad52da5f0264")
+ (revision "1"))
+ (package
+ (name "mmap-allocator")
+ (version (git-version "0.10.1" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/mmap_allocator.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1f30b2kpwwzh6333s0qi5samk458ghbnvyycf6rwx6n6j7xswhbw"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; no configure script
+ (add-before 'install 'pre-install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (substitute* "Makefile"
+ (("HEADERS=") "HEADERS=mmappable_vector.h ")
+ (("/usr") out))
+ (mkdir-p (string-append out "/lib"))
+ (mkdir (string-append out "/include"))
+ #t))))
+ #:test-target "test"))
+ (home-page "")
+ (synopsis "")
+ (description "")
+ (license license:lgpl2.0+)))) ; README just says "lpgl".