diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 81 |
1 files changed, 81 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f6bc544a63..76a1c17737 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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") |