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gnu: roary: Add bash-minimal to inputs.

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* gnu/packages/bioinformatics.scm (roary): Delete trailing #t.
[inputs]: Add bash-minimal.  Remove labels.

Change-Id: Id5ea1b12e2fa641d96a762f5f3b89edbd43a4ffa
This commit is contained in:
Maxim Cournoyer 2023-10-20 01:06:22 -04:00 • committed by Ludovic Courtès
parent 3fbd948450
commit f1aa06f0b7
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1 changed files with 32 additions and 34 deletions
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gnu/packages/bioinformatics.scm
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@ -9366,8 +9366,7 @@ partial genes, and identifies translation initiation sites.")
(for-each (lambda (file) (for-each (lambda (file)
(display file)(display "\n") (display file)(display "\n")
(invoke "perl" file)) (invoke "perl" file))
(find-files "t" ".*\\.t$")) (find-files "t" ".*\\.t$"))))
#t))
(replace 'install (replace 'install
;; There is no 'install' target in the Makefile. ;; There is no 'install' target in the Makefile.
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
@ -9378,8 +9377,7 @@ partial genes, and identifies translation initiation sites.")
(mkdir-p bin) (mkdir-p bin)
(mkdir-p perl) (mkdir-p perl)
(copy-recursively "bin" bin) (copy-recursively "bin" bin)
(copy-recursively "lib" perl) (copy-recursively "lib" perl))))
#t)))
(add-after 'install 'wrap-programs (add-after 'install 'wrap-programs
(lambda* (#:key inputs outputs #:allow-other-keys) (lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")) (let* ((out (assoc-ref outputs "out"))
@ -9405,39 +9403,39 @@ partial genes, and identifies translation initiation sites.")
(,(string-append r-site-lib ":" out "/site-library/")))) (,(string-append r-site-lib ":" out "/site-library/"))))
(wrap-program file (wrap-program file
`("PATH" ":" prefix `("PATH" ":" prefix
(,(string-append coreutils-path ":" out "/bin")))))) (,(string-append coreutils-path ":" out "/bin")))))))))))
#t)))))
(native-inputs (native-inputs
(list perl-env-path perl-test-files perl-test-most perl-test-output)) (list perl-env-path perl-test-files perl-test-most perl-test-output))
(inputs (inputs
`(("perl-array-utils" ,perl-array-utils) (list bash-minimal
("bioperl" ,bioperl-minimal) perl-array-utils
("perl-digest-md5-file" ,perl-digest-md5-file) bioperl-minimal
("perl-exception-class" ,perl-exception-class) perl-digest-md5-file
("perl-file-find-rule" ,perl-file-find-rule) perl-exception-class
("perl-file-grep" ,perl-file-grep) perl-file-find-rule
("perl-file-slurper" ,perl-file-slurper) perl-file-grep
("perl-file-which" ,perl-file-which) perl-file-slurper
("perl-graph" ,perl-graph) perl-file-which
("perl-graph-readwrite" ,perl-graph-readwrite) perl-graph
("perl-log-log4perl" ,perl-log-log4perl) perl-graph-readwrite
("perl-moose" ,perl-moose) perl-log-log4perl
("perl-perlio-utf8_strict" ,perl-perlio-utf8_strict) perl-moose
("perl-text-csv" ,perl-text-csv) perl-perlio-utf8_strict
("bedtools" ,bedtools) perl-text-csv
("cd-hit" ,cd-hit) bedtools
("blast+" ,blast+) cd-hit
("mcl" ,mcl) blast+
("parallel" ,parallel) mcl
("prank" ,prank) parallel
("mafft" ,mafft) prank
("fasttree" ,fasttree) mafft
("grep" ,grep) fasttree
("sed" ,sed) grep
("gawk" ,gawk) sed
("r-minimal" ,r-minimal) gawk
("r-ggplot2" ,r-ggplot2) r-minimal
("coreutils" ,coreutils))) r-ggplot2
coreutils))
(home-page "https://sanger-pathogens.github.io/Roary/") (home-page "https://sanger-pathogens.github.io/Roary/")
(synopsis "High speed stand-alone pan genome pipeline") (synopsis "High speed stand-alone pan genome pipeline")
(description (description