* 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
