(name . guix-patches@gnu.org)(address . guix-patches@gnu.org)
398fc66441a34468a7c66370abb8f923@mdc-berlin.de
Add phyml package tools.
- Done
Details
- 4 participants
- MadalinIonel.Patrascu@mdc-berlin.de
- M?d?lin Ionel Patra?cu
- Ricardo Wurmus
- Ricardo Wurmus
- Owner
- unassigned
- Submitted by
- MadalinIonel.Patrascu@mdc-berlin.de
- Severity
- normal
M
M
Re: [ext] bug#56999: Acknowledgement (Add phyml package tools.)
(name . 56999@debbugs.gnu.org)(address . 56999@debbugs.gnu.org)(name . Ricardo.Wurmus@mdc-berlin.de)(address . Ricardo.Wurmus@mdc-berlin.de)
d03f5f3979974bffa133260aa135df40@mdc-berlin.de
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:
All the best,
M?d?lin!
________________________________
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.)
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M
[PATCH 1/4] gnu: Add phyml.
(address . 56999@debbugs.gnu.org)
20220805093306.21767-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (phyml): New variable.
---
gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++
1 file changed, 37 insertions(+)
Toggle diff (52 lines)
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
M
[PATCH 2/4] gnu: Add phyml-mpi.
(address . 56999@debbugs.gnu.org)
20220805093306.21767-2-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (phyml-mpi): New variable.
---
gnu/packages/bioinformatics.scm | 11 +++++++++++
1 file changed, 11 insertions(+)
Toggle diff (24 lines)
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
M
[PATCH 3/4] gnu: Add phyml-phyrex.
(address . 56999@debbugs.gnu.org)
20220805093306.21767-3-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (phyml-phyrex): New variable.
---
gnu/packages/bioinformatics.scm | 7 +++++++
1 file changed, 7 insertions(+)
Toggle diff (20 lines)
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
M
[PATCH 4/4] nu: Add phyml-rf.
(address . 56999@debbugs.gnu.org)
20220805093306.21767-4-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (phyml-rf): New variable.
---
gnu/packages/bioinformatics.scm | 7 +++++++
1 file changed, 7 insertions(+)
Toggle diff (20 lines)
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
R
Re: [bug#56999] [PATCH 1/4] gnu: Add phyml.
(name . M?d?lin Ionel Patra?cu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 56999@debbugs.gnu.org)
875yj32m0z.fsf@elephly.net
M?d?lin Ionel Patra?cu <madalinionel.patrascu@mdc-berlin.de> writes:
Toggle quote (2 lines)
> * gnu/packages/bioinformatics.scm (phyml): New variable.
Thanks for the patch.
Toggle quote (16 lines)
> + "@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
R
Re: [ext] bug#56999: Acknowledgement (Add phyml package tools.)
(name . Patrascu, Madalin Ionel)(address . MadalinIonel.Patrascu@mdc-berlin.de)(name . 56999-done@debbugs.gnu.org)(address . 56999@debbugs.gnu.org)
871qtr2f3n.fsf@mdc-berlin.de
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
R
Add phyml package tools
(address . 56999-done@debbugs.gnu.org)
87o7trbtyj.fsf@mdc-berlin.de
Closing.
--
Ricardo
Closed
?