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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.
This commit is contained in:
Ben Woodcroft 2017-05-21 22:33:05 +01:00
parent 7569613076
commit 74297231be
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1 changed files with 14 additions and 11 deletions
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@ -2551,7 +2551,7 @@ Illumina, Roche 454, and the SOLiD platform.")
(define-public fraggenescan (define-public fraggenescan
(package (package
(name "fraggenescan") (name "fraggenescan")
(version "1.20") (version "1.30")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
@ -2559,7 +2559,7 @@ Illumina, Roche 454, and the SOLiD platform.")
(string-append "mirror://sourceforge/fraggenescan/" (string-append "mirror://sourceforge/fraggenescan/"
"FragGeneScan" version ".tar.gz")) "FragGeneScan" version ".tar.gz"))
(sha256 (sha256
(base32 "1zzigqmvqvjyqv4945kv6nc5ah2xxm1nxgrlsnbzav3f5c0n0pyj")))) (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:phases `(#:phases
@ -2574,6 +2574,7 @@ Illumina, Roche 454, and the SOLiD platform.")
(string-append "system(\"" (which "rm"))) (string-append "system(\"" (which "rm")))
(("system\\(\"mv") (("system\\(\"mv")
(string-append "system(\"" (which "mv"))) (string-append "system(\"" (which "mv")))
(("\\\"awk") (string-append "\"" (which "awk")))
;; This script and other programs expect the training files ;; This script and other programs expect the training files
;; to be in the non-standard location bin/train/XXX. Change ;; to be in the non-standard location bin/train/XXX. Change
;; this to be share/fraggenescan/train/XXX instead. ;; this to be share/fraggenescan/train/XXX instead.
@ -2583,10 +2584,7 @@ Illumina, Roche 454, and the SOLiD platform.")
"train/\".$FGS_train_file;"))) "train/\".$FGS_train_file;")))
(substitute* "run_hmm.c" (substitute* "run_hmm.c"
(("^ strcat\\(train_dir, \\\"train/\\\"\\);") (("^ strcat\\(train_dir, \\\"train/\\\"\\);")
(string-append " strcpy(train_dir, \"" share "/train/\");"))) (string-append " strcpy(train_dir, \"" share "/train/\");"))))
(substitute* "post_process.pl"
(("^my \\$dir = substr.*")
(string-append "my $dir = \"" share "\";"))))
#t)) #t))
(replace 'build (replace 'build
(lambda _ (and (zero? (system* "make" "clean")) (lambda _ (and (zero? (system* "make" "clean"))
@ -2598,8 +2596,6 @@ Illumina, Roche 454, and the SOLiD platform.")
(share (string-append out "/share/fraggenescan/train"))) (share (string-append out "/share/fraggenescan/train")))
(install-file "run_FragGeneScan.pl" bin) (install-file "run_FragGeneScan.pl" bin)
(install-file "FragGeneScan" bin) (install-file "FragGeneScan" bin)
(install-file "FGS_gff.py" bin)
(install-file "post_process.pl" bin)
(copy-recursively "train" share)))) (copy-recursively "train" share))))
(delete 'check) (delete 'check)
(add-after 'install 'post-install-check (add-after 'install 'post-install-check
@ -2607,8 +2603,9 @@ Illumina, Roche 454, and the SOLiD platform.")
;; output files gets created. ;; output files gets created.
(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")))
(bin (string-append out "/bin/"))) (bin (string-append out "/bin/"))
(and (zero? (system* (string-append bin "run_FragGeneScan.pl") (frag (string-append bin "run_FragGeneScan.pl")))
(and (zero? (system* frag ; Test complete genome.
"-genome=./example/NC_000913.fna" "-genome=./example/NC_000913.fna"
"-out=./test2" "-out=./test2"
"-complete=1" "-complete=1"
@ -2616,7 +2613,13 @@ Illumina, Roche 454, and the SOLiD platform.")
(file-exists? "test2.faa") (file-exists? "test2.faa")
(file-exists? "test2.ffn") (file-exists? "test2.ffn")
(file-exists? "test2.gff") (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 (inputs
`(("perl" ,perl) `(("perl" ,perl)
("python" ,python-2))) ;not compatible with python 3. ("python" ,python-2))) ;not compatible with python 3.