diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 212 |
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". |