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gnu: Add fraggenescan. 

* gnu/packages/bioinformatics.scm (fraggenescan): New variable.
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Ben Woodcroft 2015-12-28 07:53:27 +10:00 committed by Leo Famulari
parent 6819a8ddd6
commit 19f4554c94
1 changed files with 81 additions and 0 deletions
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@ -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")