Add phyml package tools.

MadalinIonel.Patrascu@mdc-berlin.de wrote 5 days ago

Recipients:(name . guix-patches@gnu.org)(address . guix-patches@gnu.org)

Message-ID:398fc66441a34468a7c66370abb8f923@mdc-berlin.de

Attachment: file

MadalinIonel.Patrascu@mdc-berlin.de wrote 5 days ago

Re: [ext] bug#56999: Acknowledgement (Add phyml package tools.)

Recipients:(name . 56999@debbugs.gnu.org)(address . 56999@debbugs.gnu.org)(name . Ricardo.Wurmus@mdc-berlin.de)(address . Ricardo.Wurmus@mdc-berlin.de)

Message-ID: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:

https://github.com/stephaneguindon/phyml/issues/166

All the best,

Mădălin!

________________________________

Sent: Friday, August 5, 2022 11:16

To: Patrascu, Madalin Ionel

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Attachment: file

Mădălin Ionel Patrașcu wrote 5 days ago

[PATCH 1/4] gnu: Add phyml.

Recipients:(address . 56999@debbugs.gnu.org)

Message-ID: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

Mădălin Ionel Patrașcu wrote 5 days ago

[PATCH 2/4] gnu: Add phyml-mpi.

Recipients:(address . 56999@debbugs.gnu.org)

Message-ID: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

Mădălin Ionel Patrașcu wrote 5 days ago

[PATCH 3/4] gnu: Add phyml-phyrex.

Recipients:(address . 56999@debbugs.gnu.org)

Message-ID: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

Mădălin Ionel Patrașcu wrote 5 days ago

[PATCH 4/4] nu: Add phyml-rf.

Recipients:(address . 56999@debbugs.gnu.org)

Message-ID: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

Ricardo Wurmus wrote 2 days ago

Re: [bug#56999] [PATCH 1/4] gnu: Add phyml.

Recipients:(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 56999@debbugs.gnu.org)

Message-ID:875yj32m0z.fsf@elephly.net

Mădălin Ionel Patrașcu <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

Ricardo Wurmus wrote 2 days ago

Re: [ext] bug#56999: Acknowledgement (Add phyml package tools.)

Recipients:(name . Patrascu, Madalin Ionel)(address . MadalinIonel.Patrascu@mdc-berlin.de)(name . 56999-done@debbugs.gnu.org)(address . 56999@debbugs.gnu.org)

Message-ID: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

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