diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 85 |
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") |