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bioinformatics: perl-prokka: Rewrite.
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* guix-science/packages/bioinformatics.scm (perl-prokka)[source]: Use
git-fetch instead of downloading from an auto-generated archive URL.
[arguments]: Use gexp; rewrite 'install phase with search-input-file
and #$output.
[inputs]: Drop labels; remove unused icedtea-8.
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@rekado
rekado committed Feb 13, 2023
1 parent 0394151 commit 05b63b9
Showing 1 changed file with 76 additions and 80 deletions.
156 changes: 76 additions & 80 deletions guix-science/packages/bioinformatics.scm
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@@ -1,5 +1,5 @@
;;; Copyright © 2016-2021 Roel Janssen <roel@gnu.org>
;;; Copyright © 2022 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2022, 2023 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This program is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
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(define-module (guix-science packages bioinformatics)
#:use-module ((guix licenses) #:prefix license:)
#:use-module ((guix build utils) #:select (alist-replace))
#:use-module (guix gexp)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages autotools)
Expand Down Expand Up @@ -1934,87 +1935,82 @@ file the lists the enriched domains and their posterior probabilities.")

(define-public perl-prokka
(package
(name "perl-prokka")
(version "1.14.0")
(source
(origin
(method url-fetch)
(uri (string-append
"https://github.com/tseemann/prokka/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1d8v52mxr61pf8pg4vw72wlq6xlfm1m0b1ds14lzr5n2xz1lgdkh"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f
(name "perl-prokka")
(version "1.14.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/tseemann/prokka/")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"03dp48d7gb1n7dp3c75mv8qis1vlzmvn6x0y5649w6hzsqn6z7yi"))))
(build-system gnu-build-system)
(arguments
(list
#:tests? #false ;there are none
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(substitute* '("bin/prokka"
"bin/prokka-abricate_to_fasta_db"
"bin/prokka-biocyc_to_fasta_db"
"bin/prokka-build_kingdom_dbs"
"bin/prokka-cdd_to_hmm"
"bin/prokka-clusters_to_hmm"
"bin/prokka-genbank_to_fasta_db"
"bin/prokka-genpept_to_fasta_db"
"bin/prokka-hamap_to_hmm"
"bin/prokka-make_tarball"
"bin/prokka-tigrfams_to_hmm"
"bin/prokka-uniprot_to_fasta_db")
(("minced ") (string-append (assoc-ref inputs "minced") "/bin/minced "))
(("blastp ") (string-append (assoc-ref inputs "blast+") "/bin/blastp "))
(("hmmscan ") (string-append (assoc-ref inputs "hmmer") "/bin/hmmscan "))
(("hmmpress ") (string-append (assoc-ref inputs "hmmer") "/bin/hmmpress "))
(("\"parallel ") (string-append "\"" (assoc-ref inputs "parallel") "/bin/parallel "))
(("aragorn ") (string-append (assoc-ref inputs "aragorn") "/bin/aragorn "))
(("prodigal ") (string-append (assoc-ref inputs "prodigal") "/bin/prodigal "))
(("cmscan ") (string-append (assoc-ref inputs "infernal") "/bin/cmscan "))
(("cmpress ") (string-append (assoc-ref inputs "infernal") "/bin/cmpress "))
(("makeblastdb ") (string-append (assoc-ref inputs "blast+") "/bin/makeblastdb ")))

(mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
(copy-recursively "bin" (string-append (assoc-ref outputs "out") "/bin"))
(mkdir-p (string-append (assoc-ref outputs "out") "/share/prokka/db"))
(copy-recursively "db" (string-append (assoc-ref outputs "out") "/share/prokka/db"))

(for-each (lambda (program)
(wrap-program program
`("PERL5LIB" ":" = (,(getenv "PERL5LIB") "$PERL5LIB"))))
(find-files (string-append (assoc-ref outputs "out") "/bin"))))))))
(inputs
`(("perl" ,perl)
("perl-time-piece" ,perl-time-piece)
("perl-xml-simple" ,perl-xml-simple)
("perl-digest-md5" ,perl-digest-md5)
("perl-module-build" ,perl-module-build)
("perl-data-dumper" ,perl-data-dumper)
("bioperl-minimal" ,bioperl-minimal)
("perl-findbin-libs" ,perl-findbin-libs)
("perl-scalar-list-utils" ,perl-scalar-list-utils)
("parallel" ,parallel)
("aragorn" ,aragorn)
("blast+" ,blast+)
("hmmer" ,hmmer)
("prodigal" ,prodigal)
("infernal" ,infernal)
("minced" ,minced)
("findutils" ,findutils)
("icedtea" ,icedtea-8)))
(native-search-paths
(list (search-path-specification
(variable "PROKKA_DBDIR")
(files '("share/prokka/db")))))
(home-page "https://github.com/tseemann/prokka")
(synopsis "Rapid prokaryotic genome annotation")
(description "This package provides tools for rapid prokaryotic
#~(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(replace 'install
(lambda* (#:key inputs #:allow-other-keys)
(substitute* '("bin/prokka"
"bin/prokka-abricate_to_fasta_db"
"bin/prokka-biocyc_to_fasta_db"
"bin/prokka-build_kingdom_dbs"
"bin/prokka-cdd_to_hmm"
"bin/prokka-clusters_to_hmm"
"bin/prokka-genbank_to_fasta_db"
"bin/prokka-genpept_to_fasta_db"
"bin/prokka-hamap_to_hmm"
"bin/prokka-make_tarball"
"bin/prokka-tigrfams_to_hmm"
"bin/prokka-uniprot_to_fasta_db")
(("\"parallel ")
(string-append "\"" (search-input-file inputs "/bin/parallel") " "))
(("(aragorn|blastp|cmpress|cmscan|hmmscan|hmmpress|makeblastdb|minced|prodigal) " _ bin)
(string-append (search-input-file inputs (string-append "/bin/" bin)) " ")))

(let ((bin (string-append #$output "/bin"))
(share (string-append #$output "/share/prokka/db")))
(mkdir-p bin)
(copy-recursively "bin" bin)
(mkdir-p share)
(copy-recursively "db" share)
(for-each (lambda (program)
(wrap-program program
`("PERL5LIB" ":" = (,(getenv "PERL5LIB") "$PERL5LIB"))))
(find-files bin))))))))
(inputs
(list aragorn
bioperl-minimal
blast+
findutils
hmmer
infernal
minced
parallel
perl
perl-data-dumper
perl-digest-md5
perl-findbin-libs
perl-module-build
perl-scalar-list-utils
perl-time-piece
perl-xml-simple
prodigal))
(native-search-paths
(list (search-path-specification
(variable "PROKKA_DBDIR")
(files '("share/prokka/db")))))
(home-page "https://github.com/tseemann/prokka")
(synopsis "Rapid prokaryotic genome annotation")
(description "This package provides tools for rapid prokaryotic
genome annotation.")
(license license:gpl3)))
(license license:gpl3)))

(define-public cgp-cavemanwrapper-1.15.2
(package
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