diff options
| author | Ben Woodcroft <donttrustben@gmail.com> | 2017-05-21 22:33:05 +0100 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2017-05-22 11:44:20 +0100 |
| commit | 74297231be34afbd9d0182651a75f40c60973ec3 (patch) | |
| tree | 8108b22f809a0846a398b505a0e4f99707fbb67d /gnu/packages/bioinformatics.scm | |
| parent | 7569613076eec7c90d32246da6cebb3543f05708 (diff) | |
gnu: fraggenescan: Update to 1.30.
* gnu/packages/bioinformatics.scm (fraggenescan): Update to 1.30.
[arguments]: Update patching of paths, install procedure. Add new test
case.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 25 |
1 files changed, 14 insertions, 11 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 35e9f359c1..9b4afbfcfb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2551,7 +2551,7 @@ Illumina, Roche 454, and the SOLiD platform.") (define-public fraggenescan (package (name "fraggenescan") - (version "1.20") + (version "1.30") (source (origin (method url-fetch) @@ -2559,7 +2559,7 @@ Illumina, Roche 454, and the SOLiD platform.") (string-append "mirror://sourceforge/fraggenescan/" "FragGeneScan" version ".tar.gz")) (sha256 - (base32 "1zzigqmvqvjyqv4945kv6nc5ah2xxm1nxgrlsnbzav3f5c0n0pyj")))) + (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj")))) (build-system gnu-build-system) (arguments `(#:phases @@ -2574,6 +2574,7 @@ Illumina, Roche 454, and the SOLiD platform.") (string-append "system(\"" (which "rm"))) (("system\\(\"mv") (string-append "system(\"" (which "mv"))) + (("\\\"awk") (string-append "\"" (which "awk"))) ;; This script and other programs expect the training files ;; to be in the non-standard location bin/train/XXX. Change ;; this to be share/fraggenescan/train/XXX instead. @@ -2583,10 +2584,7 @@ Illumina, Roche 454, and the SOLiD platform.") "train/\".$FGS_train_file;"))) (substitute* "run_hmm.c" (("^ strcat\\(train_dir, \\\"train/\\\"\\);") - (string-append " strcpy(train_dir, \"" share "/train/\");"))) - (substitute* "post_process.pl" - (("^my \\$dir = substr.*") - (string-append "my $dir = \"" share "\";")))) + (string-append " strcpy(train_dir, \"" share "/train/\");")))) #t)) (replace 'build (lambda _ (and (zero? (system* "make" "clean")) @@ -2598,8 +2596,6 @@ Illumina, Roche 454, and the SOLiD platform.") (share (string-append out "/share/fraggenescan/train"))) (install-file "run_FragGeneScan.pl" bin) (install-file "FragGeneScan" bin) - (install-file "FGS_gff.py" bin) - (install-file "post_process.pl" bin) (copy-recursively "train" share)))) (delete 'check) (add-after 'install 'post-install-check @@ -2607,8 +2603,9 @@ Illumina, Roche 454, and the SOLiD platform.") ;; output files gets created. (lambda* (#:key outputs #:allow-other-keys) (let* ((out (string-append (assoc-ref outputs "out"))) - (bin (string-append out "/bin/"))) - (and (zero? (system* (string-append bin "run_FragGeneScan.pl") + (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" @@ -2616,7 +2613,13 @@ Illumina, Roche 454, and the SOLiD platform.") (file-exists? "test2.faa") (file-exists? "test2.ffn") (file-exists? "test2.gff") - (file-exists? "test2.out")))))))) + (file-exists? "test2.out") + (zero? (system* ; Test incomplete sequences. + frag + "-genome=./example/NC_000913-fgs.ffn" + "-out=out" + "-complete=0" + "-train=454_30"))))))))) (inputs `(("perl" ,perl) ("python" ,python-2))) ;not compatible with python 3. |