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gnu: fraggenescan: Use INVOKE. 

* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in
build phases and return #T unconditionally.
master
Ricardo Wurmus 2018-11-08 08:58:46 +01:00
parent c098c49b3e
commit e438c96558
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GPG Key ID: 197A5888235FACAC
1 changed files with 22 additions and 17 deletions
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gnu/packages/bioinformatics.scm
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@ -2716,8 +2716,10 @@ Illumina, Roche 454, and the SOLiD platform.")
(string-append " strcpy(train_dir, \"" share "/train/\");"))))
#t))
(replace 'build
(lambda _ (and (zero? (system* "make" "clean"))
(zero? (system* "make" "fgs")))))
(lambda _
(invoke "make" "clean")
(invoke "make" "fgs")
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append (assoc-ref outputs "out")))
@ -2734,21 +2736,24 @@ Illumina, Roche 454, and the SOLiD platform.")
(let* ((out (string-append (assoc-ref outputs "out")))
(bin (string-append out "/bin/"))
(frag (string-append bin "run_FragGeneScan.pl")))
(and (zero? (system* frag ; Test complete genome.
"-genome=./example/NC_000913.fna"
"-out=./test2"
"-complete=1"
"-train=complete"))
(file-exists? "test2.faa")
(file-exists? "test2.ffn")
(file-exists? "test2.gff")
(file-exists? "test2.out")
(zero? (system* ; Test incomplete sequences.
frag
"-genome=./example/NC_000913-fgs.ffn"
"-out=out"
"-complete=0"
"-train=454_30")))))))))
;; Test complete genome.
(invoke frag
"-genome=./example/NC_000913.fna"
"-out=./test2"
"-complete=1"
"-train=complete")
(unless (and (file-exists? "test2.faa")
(file-exists? "test2.ffn")
(file-exists? "test2.gff")
(file-exists? "test2.out"))
(error "Expected files do not exist."))
;; Test incomplete sequences.
(invoke frag
"-genome=./example/NC_000913-fgs.ffn"
"-out=out"
"-complete=0"
"-train=454_30")
#t))))))
(inputs
`(("perl" ,perl)
("python" ,python-2))) ;not compatible with python 3.