diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 90 |
1 files changed, 0 insertions, 90 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9b30247594..3223d6eea8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3660,96 +3660,6 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.") (license license:bsd-3))) -(define-public fraggenescan - (package - (name "fraggenescan") - (version "1.30") - (source - (origin - (method url-fetch) - (uri - (string-append "mirror://sourceforge/fraggenescan/" - "FragGeneScan" version ".tar.gz")) - (sha256 - (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj")))) - (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"))) - (("\\\"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. - (("^\\$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/\");")))) - #t)) - (replace 'build - (lambda _ - (invoke "make" "clean") - (invoke "make" "fgs") - #t)) - (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) - (copy-recursively "train" share)) - #t)) - (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/")) - (frag (string-append bin "run_FragGeneScan.pl"))) - ;; Test complete genome. - (invoke frag - "-genome=./example/NC_000913.fna" - "-out=./test2" - "-complete=1" - "-train=complete") - (unless (and (file-exists? "test2.faa") - (file-exists? "test2.ffn") - (file-exists? "test2.gff") - (file-exists? "test2.out")) - (error "Expected files do not exist.")) - ;; Test incomplete sequences. - (invoke frag - "-genome=./example/NC_000913-fgs.ffn" - "-out=out" - "-complete=0" - "-train=454_30") - #t)))))) - (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 fxtract (let ((util-commit "776ca85a18a47492af3794745efcb4a905113115")) (package |