[PATCH 3/4] gnu: Add barrnap.

[Ben Woodcroft <donttrustben@gmail.com>]

* gnu/packages/bioinformatics.scm (barrnap): New variable.
---
 gnu/packages/bioinformatics.scm | 67 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 961f0b2..4541791 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -268,6 +268,73 @@ instance, it implements several methods to assess contig-wise read coverage.")
 BAM files.")
     (license license:expat)))
 
+(define-public barrnap
+  (package
+   (name "barrnap")
+   (version "0.7")
+   (source
+    (origin
+      (method url-fetch)
+      (uri (string-append
+            "https://github.com/tseemann/barrnap/archive/"
+            version ".tar.gz"))
+      (file-name (string-append name "-" version ".tar.gz"))
+      (sha256
+       (base32
+        "16y040np76my3y82hgk4yy790smbsk4h8d60d5swlv7ha3i768gg"))
+      (modules '((guix build utils)))
+      ;; Remove pre-built binaries.
+      (snippet '(begin
+                  (delete-file-recursively "binaries")
+                  #t))))
+   (build-system gnu-build-system)
+   (arguments
+    `(#:test-target "test"
+      #:phases
+      (modify-phases %standard-phases
+        (add-after 'unpack 'patch-nhmer-path
+          (lambda* (#:key inputs #:allow-other-keys)
+            (substitute* "bin/barrnap"
+              (("^my \\$NHMMER = .*")
+               (string-append "my $NHMMER = '"
+                              (assoc-ref inputs "hmmer")
+                              "/bin/nhmmer';\n")))
+            #t))
+        (delete 'configure)
+        (delete 'build)
+        (replace 'install
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let* ((out  (assoc-ref outputs "out"))
+                   (bin  (string-append out "/bin"))
+                                        ;(path (getenv "PATH"))
+                   (share (string-append out "/share/barrnap/db"))
+                   (binary "bin/barrnap"))
+              (substitute* binary
+                (("^my \\$DBDIR = .*")
+                 (string-append "my $DBDIR = '" share "';\n")))
+              (install-file binary bin)
+              (mkdir-p share)
+              (copy-recursively "db" share))
+            #t)))))
+   (inputs
+    `(("perl" ,perl)
+      ("hmmer" ,hmmer)))
+   (home-page "https://github.com/tseemann/barrnap")
+   (synopsis "Ribosomal RNA predictor")
+   (description
+    "Barrnap predicts the location of ribosomal RNA genes in genomes.  It
+supports bacteria (5S, 23S, 16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,
+16S) and eukaryotes (5S, 5.8S, 28S, 18S).  It takes FASTA DNA sequence as input,
+and write GFF3 as output.  It uses the NHMMER tool that comes with HMMER for
+HMM searching in RNA:DNA style.")
+   (license (list license:gpl3
+                  ;; The Rfam HMMs are under cc0, and the SILVA-derived HMMs are
+                  ;; academic-only.
+                  license:cc0
+                  (license:non-copyleft
+                   "file:///LICENSE.SILVA"
+                   "See LICENSE.SILVA in the distribution.")))))
+
 (define-public bcftools
   (package
     (name "bcftools")
-- 
2.10.2