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authorEfraim Flashner2022-01-23 15:22:20 +0200
committerEfraim Flashner2022-01-23 16:03:39 +0200
commitac49186339b9ee5bfeeb0e06c24cbd7ff9bc36f9 (patch)
tree32a919c2ee89c6180e7f303328b6f25c29332b1c
parentf142f16d52fbea868651b143d6e2a5d3785281f8 (diff)
downloadguix-bioinformatics-ac49186339b9ee5bfeeb0e06c24cbd7ff9bc36f9.tar.gz
gn: Add verkko.
-rw-r--r--gn/packages/bioinformatics.scm147
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)))