[-- Attachment #1: Type: text/plain, Size: 1300 bytes --] Dear reviewer, This package requires to do the .configure --argument and make for building of each tool. I already tried to specific make targets, but didn't help. Also the PhyTime has issues with the building, more you can check here: https://github.com/stephaneguindon/phyml/issues/166 All the best, Mădălin! ________________________________ From: GNU bug Tracking System <help-debbugs@gnu.org> Sent: Friday, August 5, 2022 11:16 To: Patrascu, Madalin Ionel Subject: [ext] bug#56999: Acknowledgement (Add phyml package tools.) Thank you for filing a new bug report with debbugs.gnu.org. This is an automatically generated reply to let you know your message has been received. Your message is being forwarded to the package maintainers and other interested parties for their attention; they will reply in due course. Your message has been sent to the package maintainer(s): guix-patches@gnu.org If you wish to submit further information on this problem, please send it to 56999@debbugs.gnu.org. Please do not send mail to help-debbugs@gnu.org unless you wish to report a problem with the Bug-tracking system. -- 56999: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=56999 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems [-- Attachment #2: Type: text/html, Size: 2798 bytes --]
* gnu/packages/bioinformatics.scm (phyml): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 00238531db..fa91f48569 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9068,6 +9068,43 @@ (define-public phylip 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")))) + (build-system gnu-build-system) + (native-inputs + (list automake + autoconf)) + (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{ +PhyTime} is another tool in the @code{PhyML} package that focuses on divergence +date estimation in a Bayesian setting. The main strengths of @code{PhyTime} lie +in its ability to accommodate for uncertrainty in the placement of fossil +calibration and the use of realistic models of rate variation along the tree. +Finally, 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") base-commit: 47a38d09696b309f6174b585465e621352444ddb -- 2.37.1
* gnu/packages/bioinformatics.scm (phyml-mpi): New variable. --- gnu/packages/bioinformatics.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fa91f48569..f448341031 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9105,6 +9105,17 @@ (define-public phyml well as @code{SPREAD}.") (license license:gpl3))) +(define-public phyml-mpi + (package (inherit phyml) + (name "phyml-mpi") + (arguments + `(#:configure-flags + (list "--enable-phyml-mpi"))) + (native-inputs + (list autoconf + automake + openmpi)))) + (define-public imp (package (name "imp") -- 2.37.1
* gnu/packages/bioinformatics.scm (phyml-phyrex): New variable. --- gnu/packages/bioinformatics.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f448341031..1cb2b49eea 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9116,6 +9116,13 @@ (define-public phyml-mpi automake openmpi)))) +(define-public phyml-phyrex + (package (inherit phyml) + (name "phyml-phyrex") + (arguments + `(#:configure-flags + (list "--enable-phyrex"))))) + (define-public imp (package (name "imp") -- 2.37.1
* gnu/packages/bioinformatics.scm (phyml-rf): New variable. --- gnu/packages/bioinformatics.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1cb2b49eea..5421a987b7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9123,6 +9123,13 @@ (define-public phyml-phyrex `(#:configure-flags (list "--enable-phyrex"))))) +(define-public phyml-rf + (package (inherit phyml) + (name "phyml-rf") + (arguments + `(#:configure-flags + (list "--enable-rf"))))) + (define-public imp (package (name "imp") -- 2.37.1
Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes: > * gnu/packages/bioinformatics.scm (phyml): New variable. Thanks for the patch. > + "@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{ > +PhyTime} is another tool in the @code{PhyML} package that focuses on divergence > +date estimation in a Bayesian setting. The main strengths of @code{PhyTime} lie > +in its ability to accommodate for uncertrainty in the placement of fossil > +calibration and the use of realistic models of rate variation along the tree. > +Finally, 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}.") The description mentions PhyTime and PhyREX, neither of which are included in this package. I’ll try to integrate this package with the definitions of phyml-mpi, phyml-phyrex, and phyml-rf that you’ve sent here. -- Ricardo
I modified the package definition like this: - build all tools in the same package by using separate build phases - remove any mention of PhyTime from the description - add texlive-* packages to build and install the PDF manual - remove the pre-built PDF manual from the sources - remove -march=native - set only x86_64 as supported An upstream bug (https://github.com/stephaneguindon/phyml/issues/173) made it impossible to remove -march=native completely, so I hope this is sufficient. -- Ricardo
Closing. -- Ricardo