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-rw-r--r--gnu/packages/bioinformatics.scm85
1 files changed, 85 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 00238531db..289079b766 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9068,6 +9068,91 @@ remove biased methylation positions for RRBS sequence files.")
programs for inferring phylogenies (evolutionary trees).")
(license license:bsd-2)))
+(define-public phyml
+ (package
+ (name "phyml")
+ (version "3.3.20220408")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/stephaneguindon/phyml")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "03hdqmnsgnzkcrp9r9ajdfkj33jgq4b86kra8ssjlrph65y344sa"))
+ (snippet
+ '(delete-file "doc/phyml-manual.pdf"))))
+ (build-system gnu-build-system)
+ (supported-systems '("x86_64-linux"))
+ (arguments
+ (let ((default-flags (list "--disable-native")))
+ `(#:phases
+ (let ((build (lambda (what)
+ (lambda args
+ (apply (assoc-ref %standard-phases 'configure)
+ (append args
+ (list #:configure-flags
+ (cons (format #false "--enable-~a" what)
+ '() #;,default-flags))))
+ (apply (assoc-ref %standard-phases 'build) args)
+ (apply (assoc-ref %standard-phases 'install) args)))))
+ (modify-phases %standard-phases
+ ;; We cannot use --disable-native; see
+ ;; https://github.com/stephaneguindon/phyml/issues/173 Instead we
+ ;; patch the code to at least get rid of -march=native.
+ (add-after 'unpack 'remove-march-native
+ (lambda _
+ (substitute* "configure.ac"
+ (("DEFAULT_VECTOR_FLAG=\"-march=native\"")
+ "DEFAULT_VECTOR_FLAG=\"-march=athlon64-sse3\"\n"))))
+ (add-after 'build 'build-manual
+ (lambda _
+ (with-directory-excursion "doc"
+ (invoke "make" "phyml-manual.pdf"))))
+ (add-after 'build-manual 'install-manual
+ (lambda* (#:key outputs #:allow-other-keys)
+ (with-directory-excursion "doc"
+ (install-file "phyml-manual.pdf"
+ (string-append (assoc-ref outputs "out")
+ "/share/doc/phyml")))))
+ (add-after 'install 'build-phyml-mpi
+ (build "phyml-mpi"))
+ (add-after 'build-phyml-mpi 'build-rf
+ (build "rf"))
+ (add-after 'build-rf 'build-phyrex
+ (build "phyrex")))))))
+ (native-inputs
+ (list automake
+ autoconf
+ openmpi
+ (texlive-updmap.cfg (list texlive-amsfonts
+ texlive-caption
+ texlive-cite
+ texlive-fonts-ec
+ texlive-grfext
+ texlive-hyperref
+ texlive-latex-fancyvrb
+ texlive-latex-graphics
+ texlive-latex-psfrag
+ texlive-xcolor))))
+ (home-page "https://github.com/stephaneguindon/phyml")
+ (synopsis "Programs for working on SAM/BAM files")
+ (description
+ "@code{PhyML} is a software package that uses modern statistical
+approaches to analyse alignments of nucleotide or amino acid sequences in a
+phylogenetic framework. The main tool in this package builds phylogenies
+under the maximum likelihood criterion. It implements a large number of
+substitution models coupled with efficient options to search the space of
+phylogenetic tree topologies. code{PhyREX} fits the
+spatial-Lambda-Fleming-Viot model to geo-referenced genetic data. This model
+is similar to the structured coalescent but assumes that individuals are
+distributed along a spatial continuum rather than discrete demes.
+@code{PhyREX} can be used to estimate population densities and rates of
+dispersal. Its output can be processed by treeannotator (from the
+@code{BEAST} package) as well as @code{SPREAD}.")
+ (license license:gpl3)))
+
(define-public imp
(package
(name "imp")