@@ 1355,6 1355,87 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from
Illumina, Roche 454, and the SOLiD platform.")
(license license:gpl3)))
+(define-public fraggenescan
+ (package
+ (name "fraggenescan")
+ (version "1.20")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append "mirror://sourceforge/fraggenescan/"
+ "FragGeneScan" version ".tar.gz"))
+ (sha256
+ (base32 "1zzigqmvqvjyqv4945kv6nc5ah2xxm1nxgrlsnbzav3f5c0n0pyj"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'build 'patch-paths
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (string-append (assoc-ref outputs "out")))
+ (share (string-append out "/share/fraggenescan/")))
+ (substitute* "run_FragGeneScan.pl"
+ (("system\\(\"rm")
+ (string-append "system(\"" (which "rm")))
+ (("system\\(\"mv")
+ (string-append "system(\"" (which "mv")))
+ ;; 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.
+ (("^\\$train.file = \\$dir.*")
+ (string-append "$train_file = \""
+ share
+ "train/\".$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 "\";"))))
+ #t))
+ (replace 'build
+ (lambda _ (and (zero? (system* "make" "clean"))
+ (zero? (system* "make" "fgs")))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (string-append (assoc-ref outputs "out")))
+ (bin (string-append out "/bin/"))
+ (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
+ ;; In lieu of 'make check', run one of the examples and check the
+ ;; 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")
+ "-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"))))))))
+ (inputs
+ `(("perl" ,perl)
+ ("python" ,python-2))) ;not compatible with python 3.
+ (home-page "https://sourceforge.net/projects/fraggenescan/")
+ (synopsis "Finds potentially fragmented genes in short reads")
+ (description
+ "FragGeneScan is a program for predicting bacterial and archaeal genes in
+short and error-prone DNA sequencing reads. It can also be applied to predict
+genes in incomplete assemblies or complete genomes.")
+ ;; GPL3+ according to private correspondense with the authors.
+ (license license:gpl3+)))
+
(define-public grit
(package
(name "grit")