(address . guix-patches@gnu.org)(name . Raoul Jean Piere Bonnal)(address . science.raoul.bonnal@gmail.com)
46f5cd81bff5fdde4a3a086c76cd2e2b41bfac36.1673102355.git.science.raoul.bonnal@gmail.com
---
gnu/packages/bioinformatics.scm | 57 +++++++++++++++++++++++++++++++++
1 file changed, 57 insertions(+)
Toggle diff (72 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6e909773a7..3b9c135c2e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3547,6 +3547,63 @@ (define-public discrover
of nucleic acid binding proteins.")
(license license:gpl3+)))
+(define-public eagle
+ (let ((commit "b8b3ae205d5f9faf99f231fe7d02ae51eaca2f8b")
+ (revision "1"))
+ (package
+ (name "eagle")
+ (version "2.4.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/poruloh/Eagle")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1pylmn3yqimq85fnqw7m702zqp4bw4bw60b2pf0xm2yh1w9grzss"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (substitute* "src/Makefile"
+ ;; replace BUILD_HOST and BUILD_TIME for deterministic build
+ (("BLAS_DIR = .*") "")
+ (("BOOST_INSTALL_DIR = .*") "")
+ (("HTSLIB_DIR = .*") "")
+ (("ZLIB_STATIC_DIR = .*") "")
+ (("LIBSTDCXX_STATIC_DIR = .*") "")
+ (("GLIBC_STATIC_DIR = .*") ""))))))
+ (properties `((upstream-name . "Eagle")))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f
+ #:parallel-build? #f
+ #:make-flags ,#~(list (string-append "-C" "src/"))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; The package's Makefile doesn't provide and "install"
+ ;; rule so di it by ourselves.
+ (let ((bin (string-append (assoc-ref outputs "out")
+ "/bin")))
+ (install-file "src/eagle" bin)))))))
+ (inputs
+ (list boost
+ openblas
+ htslib))
+ (home-page "https://alkesgroup.broadinstitute.org/Eagle/")
+ (synopsis "Statistical estimation of haplotypes from genotype data")
+ (description "Eagle estimates haplotype phase either within a genotyped
+cohort or using a phased reference panel. It uses a very fast HMM-based algorithm
+that improves speed and accuracy over existing methods via two key ideas: a new data
+structure based on the positional Burrows-Wheeler transform and a rapid search
+algorithm that explores only the most relevant paths through the HMM. It supports
+phasing sequence data with or without a reference and also supports phasing chrX.")
+ (license license:gpl3+))))
+
(define-public eigensoft
(package
(name "eigensoft")
base-commit: 24ad9a9a48ca4f51505912224217a2a9688c7fa0
--
2.38.1