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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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GPG key ID: 090B11993D9AEBB5
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 @@ (define-public roary
(for-each (lambda (file)
(display file)(display "\n")
(invoke "perl" file))
(find-files "t" ".*\\.t$"))
#t))
(find-files "t" ".*\\.t$"))))
(replace 'install
;; There is no 'install' target in the Makefile.
(lambda* (#:key outputs #:allow-other-keys)
@ -9378,8 +9377,7 @@ (define-public roary
(mkdir-p bin)
(mkdir-p perl)
(copy-recursively "bin" bin)
(copy-recursively "lib" perl)
#t)))
(copy-recursively "lib" perl))))
(add-after 'install 'wrap-programs
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@ -9405,39 +9403,39 @@ (define-public roary
(,(string-append r-site-lib ":" out "/site-library/"))))
(wrap-program file
`("PATH" ":" prefix
(,(string-append coreutils-path ":" out "/bin"))))))
#t)))))
(,(string-append coreutils-path ":" out "/bin")))))))))))
(native-inputs
(list perl-env-path perl-test-files perl-test-most perl-test-output))
(inputs
`(("perl-array-utils" ,perl-array-utils)
("bioperl" ,bioperl-minimal)
("perl-digest-md5-file" ,perl-digest-md5-file)
("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-minimal" ,r-minimal)
("r-ggplot2" ,r-ggplot2)
("coreutils" ,coreutils)))
(list bash-minimal
perl-array-utils
bioperl-minimal
perl-digest-md5-file
perl-exception-class
perl-file-find-rule
perl-file-grep
perl-file-slurper
perl-file-which
perl-graph
perl-graph-readwrite
perl-log-log4perl
perl-moose
perl-perlio-utf8_strict
perl-text-csv
bedtools
cd-hit
blast+
mcl
parallel
prank
mafft
fasttree
grep
sed
gawk
r-minimal
r-ggplot2
coreutils))
(home-page "https://sanger-pathogens.github.io/Roary/")
(synopsis "High speed stand-alone pan genome pipeline")
(description