bioinformatics: Add mmseqs2.

* guix-science/packages/bioinformatics.scm (mmseqs2): New variable.

1 files changed, 46 insertions, 0 deletions

diff --git a/guix-science/packages/bioinformatics.scm b/guix-science/packages/bioinformatics.scm
index 92061a3..781358b 100644
--- a/guix-science/packages/bioinformatics.scm
+++ b/guix-science/packages/bioinformatics.scm
@@ -2388,6 +2388,52 @@ array-based and next-generation sequence data, and genomic
 annotations.")
    (license license:expat)))
 
+(define-public mmseqs2
+  ;; Upstream tags use a combination of version and short commit ID.
+  (let ((commit "8cc5ce367b5638c4306c2d7cfc652dd099a4643f")
+        (version "18"))
+    (package
+      (name "mmseqs2")
+      (version version)
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/soedinglab/MMseqs2")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1fw067j0plq5z5nsxpf1hsqk008lhjrb76vvsy3l795a9q06vry4"))))
+      (build-system cmake-build-system)
+      (arguments
+       (list
+        #:configure-flags
+        #~(list "-DNATIVE_ARCH:BOOL=OFF")
+        #:phases
+        #~(modify-phases %standard-phases
+            (delete 'check)
+            (add-after 'install 'check
+              (lambda* (#:key tests? #:allow-other-keys)
+                (when tests?
+                  (let ((mmseqs (string-append #$output "/bin/mmseqs")))
+                    (with-directory-excursion "../source/examples"
+                      (invoke mmseqs "easy-cluster" "DB.fasta" "clusterRes"
+                              "tmp")
+                      (invoke mmseqs
+                              "easy-search"
+                              "QUERY.fasta"
+                              "DB.fasta"
+                              "alnRes"
+                              "tmp")))))))))
+      (inputs (list bzip2 zlib))
+      (native-inputs (list perl))
+      (home-page "https://mmseqs.com/")
+      (synopsis "Ultra fast and sensitive search and clustering suite")
+      (description
+       "MMseqs2 (Many-against-Many sequence searching) is a software suite to
+search and cluster huge protein and nucleotide sequence sets.")
+      (license license:expat))))
+
 (define-public booster
   ;; Use latest upstream commit, which fixes a segfault issue.
   (let ((commit "b9eee3213b6b75a9b066a82ec0558817f898df1b")