ryan77627/guix
1
0
Fork 0
mirror of https://git.in.rschanz.org/ryan77627/guix.git synced 2025-01-27 04:59:27 -05:00
Code Issues Projects Releases Packages Wiki Activity Actions

gnu: fraggenescan: Use INVOKE.

Browse source 
* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in
build phases and return #T unconditionally.
This commit is contained in:
Ricardo Wurmus 2018-11-08 08:58:46 +01:00
parent c098c49b3e
commit e438c96558
No known key found for this signature in database
GPG key ID: 197A5888235FACAC
1 changed files with 22 additions and 17 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

39
gnu/packages/bioinformatics.scm
View file

@ -2716,8 +2716,10 @@ (define-public fraggenescan
(string-append " strcpy(train_dir, \"" share "/train/\");")))) (string-append " strcpy(train_dir, \"" share "/train/\");"))))
#t)) #t))
(replace 'build (replace 'build
(lambda _ (and (zero? (system* "make" "clean")) (lambda _
(zero? (system* "make" "fgs"))))) (invoke "make" "clean")
(invoke "make" "fgs")
#t))
(replace 'install (replace 'install
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append (assoc-ref outputs "out"))) (let* ((out (string-append (assoc-ref outputs "out")))
@ -2734,21 +2736,24 @@ (define-public fraggenescan
(let* ((out (string-append (assoc-ref outputs "out"))) (let* ((out (string-append (assoc-ref outputs "out")))
(bin (string-append out "/bin/")) (bin (string-append out "/bin/"))
(frag (string-append bin "run_FragGeneScan.pl"))) (frag (string-append bin "run_FragGeneScan.pl")))
(and (zero? (system* frag ; Test complete genome. ;; Test complete genome.
"-genome=./example/NC_000913.fna" (invoke frag
"-out=./test2" "-genome=./example/NC_000913.fna"
"-complete=1" "-out=./test2"
"-train=complete")) "-complete=1"
(file-exists? "test2.faa") "-train=complete")
(file-exists? "test2.ffn") (unless (and (file-exists? "test2.faa")
(file-exists? "test2.gff") (file-exists? "test2.ffn")
(file-exists? "test2.out") (file-exists? "test2.gff")
(zero? (system* ; Test incomplete sequences. (file-exists? "test2.out"))
frag (error "Expected files do not exist."))
"-genome=./example/NC_000913-fgs.ffn" ;; Test incomplete sequences.
"-out=out" (invoke frag
"-complete=0" "-genome=./example/NC_000913-fgs.ffn"
"-train=454_30"))))))))) "-out=out"
"-complete=0"
"-train=454_30")
#t))))))
(inputs (inputs
`(("perl" ,perl) `(("perl" ,perl)
("python" ,python-2))) ;not compatible with python 3. ("python" ,python-2))) ;not compatible with python 3.