diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 71 |
1 files changed, 71 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1837ad0bc3..6733fcd574 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15859,6 +15859,77 @@ containing the reference genome as well.") ;; See https://github.com/dpryan79/MethylDackel/issues/85 (license license:expat))) +;; This package bundles PCRE 8.02 and cannot be built with the current +;; version. +(define-public phast + (package + (name "phast") + (version "1.5") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/CshlSiepelLab/phast") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10lpbllvny923jjbbyrpxahhd1m5h7sbj9gx7rd123rg10mlidki")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags + (list "CC=gcc" + (string-append "DESTDIR=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Fix syntax + (substitute* "test/Makefile" + ((" ") " ")) + (substitute* "Makefile" + (("CLAPACKPATH=/usr/lib") + (string-append "CLAPACKPATH=" + (assoc-ref inputs "clapack") "/lib"))) + ;; Renaming the libraries is not necessary with our version of + ;; CLAPACK. + (substitute* "src/lib/Makefile" + (("ifdef CLAPACKPATH") "ifdef UNNECESSARY")) + (substitute* "src/make-include.mk" + (("-lblaswr") "-lblas") + (("-ltmg") "-ltmglib") + (("liblapack.a") "liblapack.so") + (("libblas.a") "libblas.so") + (("libf2c.a") "libf2c.so")) + (substitute* "src/Makefile" + (("/opt") "/share") + (("/usr/") "/")) + #t)) + (replace 'check + (lambda _ + (setenv "PATH" + (string-append (getcwd) "/bin:" (getenv "PATH"))) + ;; Disable broken test + (substitute* "test/Makefile" + ((".*if.*hmrc_summary" m) (string-append "#" m))) + ;; Only run the msa_view tests because the others fail for + ;; unknown reasons. + (invoke "make" "-C" "test" "msa_view")))))) + (inputs + `(("clapack" ,clapack))) + (native-inputs + `(("perl" ,perl))) + (home-page "http://compgen.cshl.edu/phast/") + (synopsis "Phylogenetic analysis with space/time models") + (description + "Phylogenetic Analysis with Space/Time models (PHAST) is a collection of +command-line programs and supporting libraries for comparative and +evolutionary genomics. Best known as the search engine behind the +Conservation tracks in the University of California, Santa Cruz (UCSC) Genome +Browser, PHAST also includes several tools for phylogenetic modeling, +functional element identification, as well as utilities for manipulating +alignments, trees and genomic annotations.") + (license license:bsd-3))) + (define-public python-gffutils ;; The latest release is older more than a year than the latest commit (let ((commit "4034c54600813b1402945e12faa91b3a53162cf1") |