gnu: Add roary.
* gnu/packages/bioinformatics.scm (roary): New variable.
This commit is contained in:
Ben Woodcroft
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608dd93267
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@ -65,6 +65,7 @@
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#:use-module (gnu packages mpi)
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#:use-module (gnu packages ncurses)
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#:use-module (gnu packages pcre)
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#:use-module (gnu packages parallel)
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#:use-module (gnu packages pdf)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages pkg-config)
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@ -3380,6 +3381,121 @@ format. It runs quickly, in an unsupervised fashion, handles gaps, handles
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partial genes, and identifies translation initiation sites.")
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(license license:gpl3+)))
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(define-public roary
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(package
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(name "roary")
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(version "3.6.8")
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(source
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(origin
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(method url-fetch)
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(uri (string-append
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"mirror://cpan/authors/id/A/AJ/AJPAGE/Bio-Roary-"
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version ".tar.gz"))
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(sha256
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(base32
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"0g0pzcv8y7n2w8q7c9q0a7s2ghkwci6w8smg9mjw4agad5cd7yaw"))))
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(build-system perl-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(delete 'configure)
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(delete 'build)
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(replace 'check
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(lambda _
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;; The tests are not run by default, so we run each test file
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;; directly.
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(setenv "PATH" (string-append (getcwd) "/bin" ":"
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(getenv "PATH")))
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(setenv "PERL5LIB" (string-append (getcwd) "/lib" ":"
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(getenv "PERL5LIB")))
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(zero? (length (filter (lambda (file)
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(display file)(display "\n")
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(not (zero? (system* "perl" file))))
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(find-files "t" ".*\\.t$"))))))
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(replace 'install
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;; There is no 'install' target in the Makefile.
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin"))
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(perl (string-append out "/lib/perl5/site_perl"))
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(roary-plots "contrib/roary_plots"))
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(mkdir-p bin)
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(mkdir-p perl)
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(copy-recursively "bin" bin)
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(copy-recursively "lib" perl)
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#t)))
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(add-after 'install 'wrap-programs
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(perl5lib (getenv "PERL5LIB"))
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(path (getenv "PATH")))
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(for-each (lambda (prog)
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(let ((binary (string-append out "/" prog)))
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(wrap-program binary
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`("PERL5LIB" ":" prefix
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(,(string-append perl5lib ":" out
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"/lib/perl5/site_perl"))))
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(wrap-program binary
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`("PATH" ":" prefix
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(,(string-append path ":" out "/bin"))))))
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(find-files "bin" ".*[^R]$"))
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(let ((file
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(string-append out "/bin/roary-create_pan_genome_plots.R"))
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(r-site-lib (getenv "R_LIBS_SITE"))
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(coreutils-path
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(string-append (assoc-ref inputs "coreutils") "/bin")))
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(wrap-program file
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`("R_LIBS_SITE" ":" prefix
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(,(string-append r-site-lib ":" out "/site-library/"))))
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(wrap-program file
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`("PATH" ":" prefix
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(,(string-append coreutils-path ":" out "/bin"))))))
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#t)))))
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(native-inputs
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`(("perl-env-path" ,perl-env-path)
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("perl-test-files" ,perl-test-files)
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("perl-test-most" ,perl-test-most)
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("perl-test-output" ,perl-test-output)))
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(inputs
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`(("perl-array-utils" ,perl-array-utils)
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("bioperl" ,bioperl-minimal)
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("perl-exception-class" ,perl-exception-class)
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("perl-file-find-rule" ,perl-file-find-rule)
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("perl-file-grep" ,perl-file-grep)
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("perl-file-slurper" ,perl-file-slurper)
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("perl-file-which" ,perl-file-which)
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("perl-graph" ,perl-graph)
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("perl-graph-readwrite" ,perl-graph-readwrite)
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("perl-log-log4perl" ,perl-log-log4perl)
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("perl-moose" ,perl-moose)
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("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict)
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("perl-text-csv" ,perl-text-csv)
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("bedtools" ,bedtools)
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("cd-hit" ,cd-hit)
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("blast+" ,blast+)
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("mcl" ,mcl)
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("parallel" ,parallel)
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("prank" ,prank)
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("mafft" ,mafft)
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("fasttree" ,fasttree)
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("grep" ,grep)
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("sed" ,sed)
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("gawk" ,gawk)
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("r" ,r)
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("r-ggplot2" ,r-ggplot2)
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("coreutils" ,coreutils)))
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(home-page "http://sanger-pathogens.github.io/Roary")
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(synopsis "High speed stand-alone pan genome pipeline")
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(description
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"Roary is a high speed stand alone pan genome pipeline, which takes
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annotated assemblies in GFF3 format (produced by the Prokka program) and
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calculates the pan genome. Using a standard desktop PC, it can analyse
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datasets with thousands of samples, without compromising the quality of the
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results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a
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single processor. Roary is not intended for metagenomics or for comparing
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extremely diverse sets of genomes.")
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(license license:gpl3)))
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(define-public raxml
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(package
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(name "raxml")
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