diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2018-11-08 08:58:46 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2018-11-08 08:58:46 +0100 |
| commit | e438c9655808c0c3f1a56b7c5a17954670fd365d (patch) | |
| tree | aa2a2c8cc1b20363a8ee76d880e63cb818a025e0 /gnu/packages/bioinformatics.scm | |
| parent | c098c49b3e249011bfd81b3623608ee85fef879f (diff) | |
| download | gnu-guix-e438c9655808c0c3f1a56b7c5a17954670fd365d.tar gnu-guix-e438c9655808c0c3f1a56b7c5a17954670fd365d.tar.gz | |
gnu: fraggenescan: Use INVOKE.
* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in
build phases and return #T unconditionally.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 39 |
1 files changed, 22 insertions, 17 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index aa2ae6c449..e1ed7117f2 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. |