gnu: Add phyml.
* gnu/packages/bioinformatics.scm (phyml): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Mădălin Ionel Patrașcu
Ricardo Wurmus
parent
d2470772c6
commit
ec6499aad2
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@ -9068,6 +9068,91 @@ remove biased methylation positions for RRBS sequence files.")
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programs for inferring phylogenies (evolutionary trees).")
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(license license:bsd-2)))
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(define-public phyml
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(package
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(name "phyml")
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(version "3.3.20220408")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/stephaneguindon/phyml")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"03hdqmnsgnzkcrp9r9ajdfkj33jgq4b86kra8ssjlrph65y344sa"))
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(snippet
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'(delete-file "doc/phyml-manual.pdf"))))
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(build-system gnu-build-system)
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(supported-systems '("x86_64-linux"))
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(arguments
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(let ((default-flags (list "--disable-native")))
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`(#:phases
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(let ((build (lambda (what)
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(lambda args
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(apply (assoc-ref %standard-phases 'configure)
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(append args
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(list #:configure-flags
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(cons (format #false "--enable-~a" what)
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'() #;,default-flags))))
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(apply (assoc-ref %standard-phases 'build) args)
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(apply (assoc-ref %standard-phases 'install) args)))))
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(modify-phases %standard-phases
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;; We cannot use --disable-native; see
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;; https://github.com/stephaneguindon/phyml/issues/173 Instead we
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;; patch the code to at least get rid of -march=native.
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(add-after 'unpack 'remove-march-native
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(lambda _
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(substitute* "configure.ac"
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(("DEFAULT_VECTOR_FLAG=\"-march=native\"")
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"DEFAULT_VECTOR_FLAG=\"-march=athlon64-sse3\"\n"))))
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(add-after 'build 'build-manual
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(lambda _
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(with-directory-excursion "doc"
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(invoke "make" "phyml-manual.pdf"))))
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(add-after 'build-manual 'install-manual
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(lambda* (#:key outputs #:allow-other-keys)
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(with-directory-excursion "doc"
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(install-file "phyml-manual.pdf"
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(string-append (assoc-ref outputs "out")
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"/share/doc/phyml")))))
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(add-after 'install 'build-phyml-mpi
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(build "phyml-mpi"))
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(add-after 'build-phyml-mpi 'build-rf
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(build "rf"))
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(add-after 'build-rf 'build-phyrex
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(build "phyrex")))))))
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(native-inputs
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(list automake
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autoconf
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openmpi
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(texlive-updmap.cfg (list texlive-amsfonts
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texlive-caption
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texlive-cite
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texlive-fonts-ec
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texlive-grfext
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texlive-hyperref
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texlive-latex-fancyvrb
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texlive-latex-graphics
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texlive-latex-psfrag
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texlive-xcolor))))
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(home-page "https://github.com/stephaneguindon/phyml")
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(synopsis "Programs for working on SAM/BAM files")
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(description
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"@code{PhyML} is a software package that uses modern statistical
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approaches to analyse alignments of nucleotide or amino acid sequences in a
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phylogenetic framework. The main tool in this package builds phylogenies
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under the maximum likelihood criterion. It implements a large number of
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substitution models coupled with efficient options to search the space of
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phylogenetic tree topologies. code{PhyREX} fits the
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spatial-Lambda-Fleming-Viot model to geo-referenced genetic data. This model
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is similar to the structured coalescent but assumes that individuals are
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distributed along a spatial continuum rather than discrete demes.
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@code{PhyREX} can be used to estimate population densities and rates of
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dispersal. Its output can be processed by treeannotator (from the
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@code{BEAST} package) as well as @code{SPREAD}.")
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(license license:gpl3)))
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(define-public imp
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(package
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(name "imp")
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