rekado pushed a commit to branch master
in repository guix.
commit e438c9655808c0c3f1a56b7c5a17954670fd365d
Author: Ricardo Wurmus <[email protected]>
Date: Thu Nov 8 08:58:46 2018 +0100
gnu: fraggenescan: Use INVOKE.
* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in
build phases and return #T unconditionally.
---
gnu/packages/bioinformatics.scm | 39 ++++++++++++++++++++++-----------------
1 file changed, 22 insertions(+), 17 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index aa2ae6c..e1ed711 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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.
