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[PATCH 4/4] gnu: Add prokka.
From: |
Ben Woodcroft |
Subject: |
[PATCH 4/4] gnu: Add prokka. |
Date: |
Sat, 3 Dec 2016 20:39:01 +1000 |
* gnu/packages/bioinformatics.scm (prokka): New variable.
---
gnu/packages/bioinformatics.scm | 110 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 110 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4541791..c4f421c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -62,6 +62,7 @@
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages java)
+ #:use-module (gnu packages less)
#:use-module (gnu packages linux)
#:use-module (gnu packages logging)
#:use-module (gnu packages machine-learning)
@@ -3743,6 +3744,115 @@ for sequences to be aligned and then, simultaneously
with the alignment,
predicts the locations of structural units in the sequences.")
(license license:gpl2+)))
+(define-public prokka
+ ;; There has been many commits since the last released version 1.11 so we
+ ;; package from git.
+ (let ((commit "1caf2394850998f89a3782cc8846dc51978faac2"))
+ (package
+ (name "prokka")
+ (version (string-append "1.11-1." (string-take commit 8)))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/tseemann/prokka.git")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "1h8dpmrcfw5z3w9sydgv4439v1wdidyq4nx247fyqahvn88rfsnj"))
+ (modules '((guix build utils)))
+ ;; Remove bundled code.
+ (snippet '(begin
+ (delete-file-recursively "binaries")
+ (delete-file-recursively "perl5")
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'build
+ (lambda _
+ (zero? (system* "bin/prokka" "--setupdb"))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Set the path to the 'db' to refer to the share directory.
+ (substitute* "bin/prokka"
+ (("^my \\$DBDIR = .*")
+ (string-append "my $DBDIR = '"
+ (assoc-ref outputs "out")
+ "/share/prokka/db';\n")))
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (prokka (string-append bin "/prokka"))
+ (share (string-append out "/share/prokka"))
+ (path (getenv "PATH"))
+ (perl5lib (getenv "PERL5LIB")))
+ (mkdir-p share)
+ (copy-recursively "db" (string-append share "/db"))
+ (install-file "bin/prokka" bin)
+ (install-file "bin/prokka-genbank_to_fasta_db" bin)
+ (wrap-program prokka
+ `("PATH" ":" prefix
+ (,(string-append path ":" out "/bin"))))
+ (for-each
+ (lambda (binary)
+ (wrap-program binary
+ `("PERL5LIB" ":" prefix
+ (,(string-append perl5lib ":" out
+ "/lib/perl5/site_perl")))))
+ (list prokka (string-append
+ bin "/prokka-genbank_to_fasta_db"))))
+ #t))
+ (delete 'check)
+ (add-after 'install 'post-install-check
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; There are no tests, instead we run a sanity check on an
+ ;; entire genome.
+ (zero? (system* "bin/prokka"
+ "--noanno"
+ "--outdir" "example-out"
+ (assoc-ref inputs "example-genome"))))))))
+ (native-inputs
+ `(("example-genome"
+ ,(origin
+ (method url-fetch)
+ (uri "http://www.ebi.ac.uk/ena/data/view/CP002565&display=fasta")
+ (file-name (string-append "ena-genome-CP002565.fasta"))
+ (sha256
+ (base32
+ "0dv3m29kgyssjc96zbmb5khkrk7cy7a66bsjk2ricwc302g5hgfy"))))))
+ (inputs
+ `(("perl" ,perl)
+ ("bioperl" ,bioperl-minimal)
+ ("blast+" ,blast+)
+ ("hmmer" ,hmmer)
+ ("aragorn" ,aragorn)
+ ("prodigal" ,prodigal)
+ ("parallel" ,parallel)
+ ("infernal" ,infernal)
+ ("barrnap" ,barrnap)
+ ("minced" ,minced)
+ ("tbl2asn" ,ncbi-tools)
+ ("grep" ,grep)
+ ("sed" ,sed)
+ ("less" ,less)
+ ("perl-time-piece" ,perl-time-piece)
+ ("perl-xml-simple" ,perl-xml-simple)
+ ("perl-digest-md5" ,perl-digest-md5)))
+ (home-page "http://www.vicbioinformatics.com/software.prokka.shtml")
+ (synopsis "Rapid prokaryotic genome annotation")
+ (description
+ "Prokka is a software tool for the rapid annotation of prokaryotic
+genomes. It produces GFF3, GBK and SQN files that are ready for editing in
+Sequin and ultimately submitted to Genbank/DDJB/ENA. ")
+ (license (list license:gpl2
+ ;; Available under various licenses.
+ (license:non-copyleft
+ "file://doc"
+ "See license files in the doc directory."))))))
+
(define-public proteinortho
(package
(name "proteinortho")
--
2.10.2