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authorBen Woodcroft <donttrustben@gmail.com>2016-07-12 16:38:13 +1000
committerBen Woodcroft <donttrustben@gmail.com>2016-08-08 22:08:17 +1000
commitceb62d5436e2254e4f05671e81b1eff589c531e1 (patch)
tree9d922f25860387d307230c55b90ea7bb0e65cdbe /gnu
parent608dd932674def26c02bb255ebabcb62442f1093 (diff)
downloadguix-ceb62d5436e2254e4f05671e81b1eff589c531e1.tar.gz
guix-ceb62d5436e2254e4f05671e81b1eff589c531e1.zip
gnu: Add roary.
* gnu/packages/bioinformatics.scm (roary): New variable.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm116
1 files changed, 116 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index df6c487198..65d7cdc275 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -65,6 +65,7 @@
#:use-module (gnu packages mpi)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages pcre)
+ #:use-module (gnu packages parallel)
#:use-module (gnu packages pdf)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
@@ -3380,6 +3381,121 @@ format. It runs quickly, in an unsupervised fashion, handles gaps, handles
partial genes, and identifies translation initiation sites.")
(license license:gpl3+)))
+(define-public roary
+ (package
+ (name "roary")
+ (version "3.6.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "mirror://cpan/authors/id/A/AJ/AJPAGE/Bio-Roary-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0g0pzcv8y7n2w8q7c9q0a7s2ghkwci6w8smg9mjw4agad5cd7yaw"))))
+ (build-system perl-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'build)
+ (replace 'check
+ (lambda _
+ ;; The tests are not run by default, so we run each test file
+ ;; directly.
+ (setenv "PATH" (string-append (getcwd) "/bin" ":"
+ (getenv "PATH")))
+ (setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
+ (getenv "PERL5LIB")))
+ (zero? (length (filter (lambda (file)
+ (display file)(display "\n")
+ (not (zero? (system* "perl" file))))
+ (find-files "t" ".*\\.t$"))))))
+ (replace 'install
+ ;; There is no 'install' target in the Makefile.
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (perl (string-append out "/lib/perl5/site_perl"))
+ (roary-plots "contrib/roary_plots"))
+ (mkdir-p bin)
+ (mkdir-p perl)
+ (copy-recursively "bin" bin)
+ (copy-recursively "lib" perl)
+ #t)))
+ (add-after 'install 'wrap-programs
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (perl5lib (getenv "PERL5LIB"))
+ (path (getenv "PATH")))
+ (for-each (lambda (prog)
+ (let ((binary (string-append out "/" prog)))
+ (wrap-program binary
+ `("PERL5LIB" ":" prefix
+ (,(string-append perl5lib ":" out
+ "/lib/perl5/site_perl"))))
+ (wrap-program binary
+ `("PATH" ":" prefix
+ (,(string-append path ":" out "/bin"))))))
+ (find-files "bin" ".*[^R]$"))
+ (let ((file
+ (string-append out "/bin/roary-create_pan_genome_plots.R"))
+ (r-site-lib (getenv "R_LIBS_SITE"))
+ (coreutils-path
+ (string-append (assoc-ref inputs "coreutils") "/bin")))
+ (wrap-program file
+ `("R_LIBS_SITE" ":" prefix
+ (,(string-append r-site-lib ":" out "/site-library/"))))
+ (wrap-program file
+ `("PATH" ":" prefix
+ (,(string-append coreutils-path ":" out "/bin"))))))
+ #t)))))
+ (native-inputs
+ `(("perl-env-path" ,perl-env-path)
+ ("perl-test-files" ,perl-test-files)
+ ("perl-test-most" ,perl-test-most)
+ ("perl-test-output" ,perl-test-output)))
+ (inputs
+ `(("perl-array-utils" ,perl-array-utils)
+ ("bioperl" ,bioperl-minimal)
+ ("perl-exception-class" ,perl-exception-class)
+ ("perl-file-find-rule" ,perl-file-find-rule)
+ ("perl-file-grep" ,perl-file-grep)
+ ("perl-file-slurper" ,perl-file-slurper)
+ ("perl-file-which" ,perl-file-which)
+ ("perl-graph" ,perl-graph)
+ ("perl-graph-readwrite" ,perl-graph-readwrite)
+ ("perl-log-log4perl" ,perl-log-log4perl)
+ ("perl-moose" ,perl-moose)
+ ("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict)
+ ("perl-text-csv" ,perl-text-csv)
+ ("bedtools" ,bedtools)
+ ("cd-hit" ,cd-hit)
+ ("blast+" ,blast+)
+ ("mcl" ,mcl)
+ ("parallel" ,parallel)
+ ("prank" ,prank)
+ ("mafft" ,mafft)
+ ("fasttree" ,fasttree)
+ ("grep" ,grep)
+ ("sed" ,sed)
+ ("gawk" ,gawk)
+ ("r" ,r)
+ ("r-ggplot2" ,r-ggplot2)
+ ("coreutils" ,coreutils)))
+ (home-page "http://sanger-pathogens.github.io/Roary")
+ (synopsis "High speed stand-alone pan genome pipeline")
+ (description
+ "Roary is a high speed stand alone pan genome pipeline, which takes
+annotated assemblies in GFF3 format (produced by the Prokka program) and
+calculates the pan genome. Using a standard desktop PC, it can analyse
+datasets with thousands of samples, without compromising the quality of the
+results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a
+single processor. Roary is not intended for metagenomics or for comparing
+extremely diverse sets of genomes.")
+ (license license:gpl3)))
+
(define-public raxml
(package
(name "raxml")