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authorEfraim Flashner2021-11-14 11:48:35 +0200
committerEfraim Flashner2021-11-14 11:56:21 +0200
commit1402f3e886dc7cf6753630b8473888b3cd25a10f (patch)
treeee86e4cbd88e4a5d171da349d0afb90968bc03c6 /gn/packages/bioinformatics.scm
parent8efe9ed0fd4bcd617d9ea3127fee73d5e4862540 (diff)
downloadguix-bioinformatics-1402f3e886dc7cf6753630b8473888b3cd25a10f.tar.gz
gn: add metaeuk
Diffstat (limited to 'gn/packages/bioinformatics.scm')
-rw-r--r--gn/packages/bioinformatics.scm63
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)))