diff options
Diffstat (limited to 'gnu/packages/perl.scm')
| -rw-r--r-- | gnu/packages/perl.scm | 96 |
1 files changed, 96 insertions, 0 deletions
diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm index 7e27ea01e7..0d4dcd6fe0 100644 --- a/gnu/packages/perl.scm +++ b/gnu/packages/perl.scm @@ -52,6 +52,7 @@ #:use-module (gnu packages base) #:use-module (gnu packages compression) #:use-module (gnu packages freedesktop) + #:use-module (gnu packages gd) #:use-module (gnu packages less) #:use-module (gnu packages ncurses) #:use-module (gnu packages perl-check) @@ -870,6 +871,101 @@ the Carp.pm module doesn't help.") ;; Either GPLv2 or the "Artistic" license. (license (list gpl2 artistic2.0)))) +(define-public circos + (package + (name "circos") + (version "0.69-9") + (source (origin + (method url-fetch) + (uri (string-append + "http://circos.ca/distribution/circos-" version ".tgz")) + (sha256 + (base32 "1ll9yxbk0v64813np0qz6h8bc53qlnhg9y1053b57xgkxgmxgn1l")) + (patches (list (search-patch "circos-remove-findbin.patch"))))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests. + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'build) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (datapath (string-append out "/share/Circos")) + (error (string-append out "/share/Circos/error")) + (fonts (string-append out "/share/Circos/fonts")) + (data (string-append out "/share/Circos/data")) + (tiles (string-append out "/share/Circos/tiles")) + (etc (string-append out "/share/Circos/etc")) + (lib (string-append out "/lib/perl5/site_perl/" + ,(package-version perl))) + (install-directory (lambda (source target) + (mkdir-p target) + (copy-recursively source target)))) + ;; Circos looks into a relative path for its configuration + ;; files. We need to provide an absolute path towards the + ;; corresponding paths in the store. + (substitute* '("bin/circos" "etc/colors_fonts_patterns.conf" + "etc/gddiag.conf" "etc/brewer.conf" "README") + (("<<include etc") (string-append "<<include " etc))) + (substitute* '("etc/colors.conf" "etc/image.black.conf" + "etc/patterns.conf" "etc/image.conf") + (("<<include ") (string-append "<<include " etc "/"))) + (substitute* '("etc/fonts.conf" "fonts/README.fonts") + (("= fonts") (string-append "= " fonts))) + (substitute* "etc/patterns.conf" + (("= tiles") (string-append "= " tiles))) + (substitute* "lib/Circos/Error.pm" + (("error/configuration.missing.txt") + (string-append error "/configuration.missing.txt"))) + (substitute* "etc/housekeeping.conf" + (("# data_path = /home/martink/circos-tutorials ") + (string-append "data_path = " datapath))) + (substitute* "lib/Circos/Configuration.pm" + (("my @possibilities = \\(") + (string-append "my @possibilities = (" + "catfile( \"" datapath "\", $arg ), " + "catfile( \"" etc "\", $arg ), " + "catfile( \"" etc "/tracks\", $arg ), "))) + (for-each install-directory + (list "error" "fonts" "data" "tiles" "etc" "lib") + (list error fonts data tiles etc lib)) + (install-file "bin/circos" bin) + #t)))))) + (propagated-inputs + `(("perl" ,perl) + ("perl-carp" ,perl-carp) + ("perl-clone" ,perl-clone) + ("perl-config-general" ,perl-config-general) + ("perl-digest-md5" ,perl-digest-md5) + ("perl-file-temp" ,perl-file-temp) + ("perl-font-ttf" ,perl-font-ttf) + ("perl-gd" ,perl-gd) + ("perl-getopt-long" ,perl-getopt-long) + ("perl-list-allutils" ,perl-list-allutils) + ("perl-math-bezier" ,perl-math-bezier) + ("perl-math-round" ,perl-math-round) + ("perl-math-vecstat" ,perl-math-vecstat) + ("perl-memoize" ,perl-memoize) + ("perl-number-format" ,perl-number-format) + ("perl-params-validate" ,perl-params-validate) + ("perl-readonly" ,perl-readonly) + ("perl-regexp-common" ,perl-regexp-common) + ("perl-set-intspan" ,perl-set-intspan) + ("perl-statistics-basic" ,perl-statistics-basic) + ("perl-svg" ,perl-svg) + ("perl-text-balanced" ,perl-text-balanced) + ("perl-text-format" ,perl-text-format) + ("perl-time-hires" ,perl-time-hires))) + (home-page "http://circos.ca/") + (synopsis "Generation of circularly composited renditions") + (description + "Circos is a program for the generation of publication-quality, circularly +composited renditions of genomic data and related annotations.") + (license gpl2+))) + (define-public perl-class-accessor (package (name "perl-class-accessor") |