GNU bug report logs - #56999
Add phyml package tools.

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Package: guix-patches;

Reported by: "MadalinIonel.Patrascu <at> mdc-berlin.de" <MadalinIonel.Patrascu <at> mdc-berlin.de>

Date: Fri, 5 Aug 2022 09:16:02 UTC

Severity: normal

Done: Ricardo Wurmus <ricardo.wurmus <at> mdc-berlin.de>

Bug is archived. No further changes may be made.

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Report forwarded to guix-patches <at> gnu.org:
bug#56999; Package guix-patches. (Fri, 05 Aug 2022 09:16:02 GMT) Full text and rfc822 format available.

Acknowledgement sent to "MadalinIonel.Patrascu <at> mdc-berlin.de" <MadalinIonel.Patrascu <at> mdc-berlin.de>:
New bug report received and forwarded. Copy sent to guix-patches <at> gnu.org. (Fri, 05 Aug 2022 09:16:02 GMT) Full text and rfc822 format available.

Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: "MadalinIonel.Patrascu <at> mdc-berlin.de"
 <MadalinIonel.Patrascu <at> mdc-berlin.de>
To: "guix-patches <at> gnu.org" <guix-patches <at> gnu.org>
Subject: Add phyml package tools.
Date: Fri, 5 Aug 2022 09:14:56 +0000
[Message part 1 (text/plain, inline)]

[Message part 2 (text/html, inline)]

Information forwarded to guix-patches <at> gnu.org:
bug#56999; Package guix-patches. (Fri, 05 Aug 2022 09:31:02 GMT) Full text and rfc822 format available.

Message #8 received at 56999 <at> debbugs.gnu.org (full text, mbox):

From: "MadalinIonel.Patrascu <at> mdc-berlin.de"
 <MadalinIonel.Patrascu <at> mdc-berlin.de>
To: "56999 <at> debbugs.gnu.org" <56999 <at> debbugs.gnu.org>
Cc: "Ricardo.Wurmus <at> mdc-berlin.de" <Ricardo.Wurmus <at> mdc-berlin.de>
Subject: Re: [ext] bug#56999: Acknowledgement (Add phyml package tools.)
Date: Fri, 5 Aug 2022 09:29:49 +0000
[Message part 1 (text/plain, inline)]
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 <at> 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.

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--
56999: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=56999
GNU Bug Tracking System
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[Message part 2 (text/html, inline)]

Information forwarded to rekado <at> elephly.net, guix-patches <at> gnu.org:
bug#56999; Package guix-patches. (Fri, 05 Aug 2022 09:34:02 GMT) Full text and rfc822 format available.

Message #11 received at 56999 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <56999 <at> debbugs.gnu.org>
Subject: [PATCH 1/4] gnu: Add phyml.
Date: Fri, 5 Aug 2022 11:33:03 +0200
* 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





Information forwarded to rekado <at> elephly.net, guix-patches <at> gnu.org:
bug#56999; Package guix-patches. (Fri, 05 Aug 2022 09:34:02 GMT) Full text and rfc822 format available.

Message #14 received at 56999 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <56999 <at> debbugs.gnu.org>
Subject: [PATCH 2/4] gnu: Add phyml-mpi.
Date: Fri, 5 Aug 2022 11:33:04 +0200
* 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





Information forwarded to rekado <at> elephly.net, guix-patches <at> gnu.org:
bug#56999; Package guix-patches. (Fri, 05 Aug 2022 09:34:02 GMT) Full text and rfc822 format available.

Message #17 received at 56999 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <56999 <at> debbugs.gnu.org>
Subject: [PATCH 3/4] gnu: Add phyml-phyrex.
Date: Fri, 5 Aug 2022 11:33:05 +0200
* 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





Information forwarded to rekado <at> elephly.net, guix-patches <at> gnu.org:
bug#56999; Package guix-patches. (Fri, 05 Aug 2022 09:34:03 GMT) Full text and rfc822 format available.

Message #20 received at 56999 <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <56999 <at> debbugs.gnu.org>
Subject: [PATCH 4/4] nu: Add phyml-rf.
Date: Fri, 5 Aug 2022 11:33:06 +0200
* 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





Information forwarded to guix-patches <at> gnu.org:
bug#56999; Package guix-patches. (Mon, 08 Aug 2022 08:11:02 GMT) Full text and rfc822 format available.

Message #23 received at 56999 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 56999 <at> debbugs.gnu.org
Subject: Re: [bug#56999] [PATCH 1/4] gnu: Add phyml.
Date: Mon, 08 Aug 2022 10:09:05 +0200
Mădălin Ionel Patrașcu <madalinionel.patrascu <at> 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




Information forwarded to guix-patches <at> gnu.org:
bug#56999; Package guix-patches. (Mon, 08 Aug 2022 10:41:01 GMT) Full text and rfc822 format available.

Message #26 received at 56999 <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <ricardo.wurmus <at> mdc-berlin.de>
To: "Patrascu, Madalin Ionel" <MadalinIonel.Patrascu <at> mdc-berlin.de>
Cc: "56999-done <at> debbugs.gnu.org" <56999 <at> debbugs.gnu.org>
Subject: Re: [ext] bug#56999: Acknowledgement (Add phyml package tools.)
Date: Mon, 8 Aug 2022 12:35:28 +0200
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




Reply sent to Ricardo Wurmus <ricardo.wurmus <at> mdc-berlin.de>:
You have taken responsibility. (Mon, 31 Oct 2022 20:49:02 GMT) Full text and rfc822 format available.

Notification sent to "MadalinIonel.Patrascu <at> mdc-berlin.de" <MadalinIonel.Patrascu <at> mdc-berlin.de>:
bug acknowledged by developer. (Mon, 31 Oct 2022 20:49:02 GMT) Full text and rfc822 format available.

Message #31 received at 56999-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <ricardo.wurmus <at> mdc-berlin.de>
To: <56999-done <at> debbugs.gnu.org>
Subject: Add phyml package tools
Date: Mon, 31 Oct 2022 21:47:38 +0100
Closing.

-- 
Ricardo




bug archived. Request was from Debbugs Internal Request <help-debbugs <at> gnu.org> to internal_control <at> debbugs.gnu.org. (Tue, 29 Nov 2022 12:24:13 GMT) Full text and rfc822 format available.

This bug report was last modified 1 year and 120 days ago.

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