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authorRicardo Wurmus <rekado@elephly.net>2020-08-10 15:48:09 +0200
committerRicardo Wurmus <rekado@elephly.net>2020-08-10 21:58:38 +0200
commita62aadf216f36fae5b1454cb5a63f6f4b259e865 (patch)
tree4af40b38fa099ea37121eaf29ecd0bab180c8434 /gnu
parent698673699e0ec501bca3abf1d455670a49cbf90e (diff)
downloadguix-a62aadf216f36fae5b1454cb5a63f6f4b259e865.tar.gz
guix-a62aadf216f36fae5b1454cb5a63f6f4b259e865.zip
gnu: Add phast.
* gnu/packages/bioinformatics.scm (phast): New variable.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm71
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")