diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 37 |
1 files changed, 14 insertions, 23 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 239b94b6c4..3387a2571a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -151,11 +151,9 @@ and several other tools.") (bin (string-append out "/bin")) (man (string-append out "/share/man/man1"))) (mkdir-p bin) - (copy-file "aragorn" - (string-append bin "/aragorn")) + (install-file "aragorn" bin) (mkdir-p man) - (copy-file "aragorn.1" - (string-append man "/aragorn.1"))) + (install-file "aragorn.1" man)) #t))))) (home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN") (synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences") @@ -1700,15 +1698,16 @@ gene predictor designed to work with assembled, aligned RNA-seq transcripts.") (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) (copy-recursively "src" (string-append out "/src")) - (mkdir (string-append out "/bin")) + (mkdir bin) ;; Add "src" directory to module lookup path. (substitute* "couger" (("from argparse") (string-append "import sys\nsys.path.append(\"" out "\")\nfrom argparse"))) - (copy-file "couger" (string-append out "/bin/couger"))) + (install-file "couger" bin)) #t)) (add-after 'install 'wrap-program @@ -2231,8 +2230,7 @@ quantitative phenotypes.") (let ((target (string-append (assoc-ref outputs "out") "/bin"))) (mkdir-p target) - (copy-file "edirect.pl" - (string-append target "/edirect.pl")) + (install-file "edirect.pl" target) #t))) (add-after 'install 'wrap-program @@ -2378,10 +2376,8 @@ ChIP-Seq, and analysis of metagenomic data.") (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (mkdir-p bin) - (copy-file "scripts/convertToEBD.py" - (string-append bin "/convertToEBD.py")) - (copy-file "bin/ExpressBetaDiversity" - (string-append bin "/ExpressBetaDiversity")) + (install-file "scripts/convertToEBD.py" bin) + (install-file "bin/ExpressBetaDiversity" bin) #t)))))) (inputs `(("python" ,python-2))) @@ -2440,10 +2436,8 @@ similarity of community members.") (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (mkdir-p bin) - (copy-file "FastTree" - (string-append bin "/FastTree")) - (copy-file "FastTreeMP" - (string-append bin "/FastTreeMP")) + (install-file "FastTree" bin) + (install-file "FastTreeMP" bin) #t)))))) (home-page "http://www.microbesonline.org/fasttree") (synopsis "Infers approximately-maximum-likelihood phylogenetic trees") @@ -4101,11 +4095,9 @@ phylogenies.") (mkdir-p bin) (mkdir-p perl) (for-each (lambda (file) - (copy-file file - (string-append bin (basename file)))) + (install-file file bin)) (find-files "." "rsem-.*")) - (copy-file "rsem_perl_utils.pm" - (string-append perl "/rsem_perl_utils.pm"))) + (install-file "rsem_perl_utils.pm" perl)) #t)) (add-after 'install 'wrap-program @@ -4336,8 +4328,7 @@ viewer.") (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (mkdir-p bin) - (copy-file "samtools" - (string-append bin "/samtools")) + (install-file "samtools" bin) #t))) (delete 'patch-tests) (delete 'configure)))))))) |