diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 63 |
1 files changed, 63 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index faf24f7..1011c7f 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 assembly) #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages bash) @@ -35,6 +36,7 @@ #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages datastructures) + #:use-module (gnu packages digest) #:use-module (gnu packages elf) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) @@ -2447,3 +2449,64 @@ capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Back when it was released, Minia produced results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).") (license license:agpl3+))) + +(define-public metaeuk + (package + (name "metaeuk") + (version "5-34c21f2") ; As seen upstream. + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/soedinglab/metaeuk") + (commit version) + (recursive? #t))) ; Only contains the tests. + (file-name (git-file-name name version)) + (sha256 + (base32 "0pqiqy3wycn9h3y699b5drd3y4zmz087bwgdxx6wbbqqipa6wk0j")) + (modules '((guix build utils))) + (snippet + '(begin + ;(delete-file-recursively "lib/mmseqs/lib/gzstream") + (delete-file-recursively "lib/mmseqs/lib/simde") + (delete-file-recursively "lib/mmseqs/lib/xxhash") + (delete-file-recursively "lib/mmseqs/lib/zstd"))))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags '("-DUSE_SYSTEM_ZSTD=YES") + #:substitutable? #f ; We want the native build. + #:tests? #f ; TODO + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-shared-libraries + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "lib/mmseqs/CMakeLists.txt" + (("libzstd\\.a") "libzstd.so") + (("libzstd_static") "libzstd_shared") + ;(("lib/gzstream") + ; (string-append (assoc-ref inputs "gzstream") "/include")) + (("lib/xxhash") + (string-append (assoc-ref inputs "xxhash") "/include")) + (("lib/simde") + (string-append (assoc-ref inputs "simde") "/include/simde"))) + #t))))) + (inputs + `(("bzip2" ,bzip2) + ("zlib" ,zlib) + ("zstd:lib" ,zstd "lib"))) + (native-inputs + `(;("gzstream" ,gzstream) + ("simde" ,simde) + ("xxd" ,xxd) + ("xxhash" ,xxhash))) + (home-page "https://github.com/soedinglab/metaeuk") + (synopsis + "Gene discovery and annotation for large-scale eukaryotic metagenomics") + (description + "MetaEuk is a modular toolkit designed for large-scale gene discovery and +annotation in eukaryotic metagenomic contigs. MetaEuk combines the fast and +sensitive homology search capabilities of +@url{https://github.com/soedinglab/MMseqs2, MMseqs2} with a dynamic programming +procedure to recover optimal exons sets. It reduces redundancies in multiple +discoveries of the same gene and resolves conflicting gene predictions on the +same strand.") + (license license:gpl3))) |