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| -rw-r--r-- | gn/packages/bioinformatics.scm | 147 |
1 files changed, 147 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 034daf0..9e94f96 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2892,3 +2892,150 @@ translocations from the commandline or with highly configureable RMT files.") "This package provides a list-like type for Python with better asymptotic performance and similar performance on small lists.") (license license:bsd-3))) + +(define-public verkko + (let ((commit "9323e71f46b0ea1725202ebe911142d0d1288c45") ; Jan 22, 2022 + (revision "1")) + (package + (name "verkko") + (version (git-version "1.0_beta" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/marbl/verkko") + (commit commit) + (recursive? #t))) ; Needs canu + (file-name (git-file-name name version)) + (sha256 + (base32 "0pb66mlz8r9hrvlcfw9zwxqzzns7221pm2z9mrjisvniwq8ggqmh")))) + (build-system gnu-build-system) + (arguments + (list + #:make-flags + #~(list (string-append "CC=" #$(cc-for-target)) + (string-append "VERSION= verkko " #$version) + "BUILDOPTIMIZED=1") + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; No configure script. + (add-after 'unpack 'chdir + (lambda _ (chdir "src"))) + (add-after 'chdir 'patch-source + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "verkko.sh" + (("\"#!/bin/sh\"") + (string-append "\"#!" (which "sh") "\"")) + ;; Hardcode the paths to some binaries + (("\\$\\(which MBG\\)") + (search-input-file inputs "/bin/MBG")) + (("\\$\\(which GraphAligner\\)") + (search-input-file inputs "/bin/GraphAligner")) + (("snakemake --nocolor") + (string-append (search-input-file + inputs + "/bin/snakemake") + " --nocolor"))) + (substitute* (find-files "Snakefiles") + (("#!/bin/sh") (string-append "#!" (which "sh")))))) + (replace 'check + (lambda* (#:key tests? inputs #:allow-other-keys) + (let ((hifi.fastq.gz (assoc-ref inputs "hifi.fastq.gz")) + (ont.fastq.gz (assoc-ref inputs "ont.fastq.gz"))) + (when tests? + (invoke "../bin/verkko" "-d" "asm" + "--hifi" hifi.fastq.gz + "--nano" ont.fastq.gz))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (with-directory-excursion "../" + (copy-recursively "bin" (string-append out "/bin")) + (copy-recursively "lib" (string-append out "/lib"))))))))) + (inputs + (list graphaligner + mbg + python-wrapper + snakemake)) + (native-inputs + `(("perl" ,perl) + ;; Provided by upstream to test the build: + ("hifi.fastq.gz" ; 118 MiB + ,(origin + (method url-fetch) + (uri "https://obj.umiacs.umd.edu/sergek/shared/ecoli_hifi_subset24x.fastq.gz") + (sha256 + (base32 "1nh5jzwnlf0r37rcgqwsjlszb8i0w5pfwp3rb5h869qp5qdlms8z")))) + ("ont.fastq.gz" ; 244 MiB + ,(origin + (method url-fetch) + (uri "https://obj.umiacs.umd.edu/sergek/shared/ecoli_ont_subset50x.fastq.gz") + (sha256 + (base32 "056pkf1dx76zs88vi4zgcbzrgvqqvlq9mpnyvmdszyhy0cj00smy")))))) + (home-page "https://github.com/marbl/verkko") + (synopsis "Hybrid genome assembly pipeline for telomere-to-telomere +assembly of PacBio HiFi and Oxford Nanopore reads") + (description "Verkko is a hybrid genome assembly pipeline developed for +telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads. Verkko +is Finnish for net, mesh and graph. Verkko uses Canu to correct remaining +errors in the HiFi reads, builds a multiplex de Bruijn graph using MBG, aligns +the Oxford Nanopore reads to the graph using GraphAligner, progressively +resolves loops and tangles first with the HiFi reads then with the aligned +Oxford Nanopore reads, and finally creates contig consensus sequences using +Canu's consensus module.") + (license license:public-domain)))) + +(define-public mbg + (package + (name "mbg") + (version "1.0.8") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/maickrau/MBG") + (commit (string-append "v" version)) + (recursive? #t))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "14p0vk6qfyf7ha8x30dk8hi16c5n8fpzi96k2vwmg17mlcf0hkgj")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ; No tests. + #:make-flags + #~(list (string-append "VERSION=" #$version)) + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; No configure script. + (add-after 'unpack 'use-packaged-inputs + (lambda* (#:key inputs #:allow-other-keys) + (let ((cxxopts (dirname (search-input-file inputs + "/include/cxxopts.hpp"))) + (concurrentqueue + (search-input-directory inputs + "/include/concurrentqueue"))) + (delete-file-recursively "cxxopts") + (delete-file-recursively "concurrentqueue") + (substitute* "makefile" + (("-Icxxopts/include") (string-append "-I" cxxopts)) + (("-Iconcurrentqueue") (string-append "-I" concurrentqueue)) + ;; No need to build statically. + (("-Wl,-Bstatic") "") + (("-static-libstdc\\+\\+") ""))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (install-file "bin/MBG" (string-append out "/bin")))))))) + (inputs (list concurrentqueue + ;; parallel-hashmap + ;; zstr + zlib)) + (native-inputs (list cxxopts)) + (home-page "https://github.com/maickrau/MBG") + (synopsis "Minimizer based sparse de Bruijn Graph constructor") + (description + "Minimizer based sparse de Bruijn Graph constructor. Homopolymer compress +input sequences, pick syncmers from hpc-compressed sequences, connect syncmers +with an edge if they are adjacent in a read, unitigify and homopolymer +decompress. Suggested input is PacBio HiFi/CCS reads.") + (license license:expat))) |