unofficial mirror of guix-patches@gnu.org 
 help / color / mirror / code / Atom feed
* [bug#56999] Add phyml package tools.
@ 2022-08-05  9:14 MadalinIonel.Patrascu
       [not found] ` <handler.56999.B.165969091927817.ack@debbugs.gnu.org>
  2022-08-05  9:33 ` [bug#56999] [PATCH 1/4] gnu: Add phyml Mădălin Ionel Patrașcu
  0 siblings, 2 replies; 8+ messages in thread
From: MadalinIonel.Patrascu @ 2022-08-05  9:14 UTC (permalink / raw)
  To: 56999

[-- Attachment #1: Type: text/plain, Size: 2 bytes --]



[-- Attachment #2: Type: text/html, Size: 830 bytes --]

^ permalink raw reply	[flat|nested] 8+ messages in thread

* [bug#56999] [ext] bug#56999: Acknowledgement (Add phyml package tools.)
       [not found] ` <handler.56999.B.165969091927817.ack@debbugs.gnu.org>
@ 2022-08-05  9:29   ` MadalinIonel.Patrascu
  2022-08-08 10:35     ` Ricardo Wurmus
  0 siblings, 1 reply; 8+ messages in thread
From: MadalinIonel.Patrascu @ 2022-08-05  9:29 UTC (permalink / raw)
  To: 56999; +Cc: Ricardo.Wurmus

[-- 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 --]

^ permalink raw reply	[flat|nested] 8+ messages in thread

* [bug#56999] [PATCH 1/4] gnu: Add phyml.
  2022-08-05  9:14 [bug#56999] Add phyml package tools MadalinIonel.Patrascu
       [not found] ` <handler.56999.B.165969091927817.ack@debbugs.gnu.org>
@ 2022-08-05  9:33 ` Mădălin Ionel Patrașcu
  2022-08-05  9:33   ` [bug#56999] [PATCH 2/4] gnu: Add phyml-mpi Mădălin Ionel Patrașcu
                     ` (3 more replies)
  1 sibling, 4 replies; 8+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-08-05  9:33 UTC (permalink / raw)
  To: 56999; +Cc: rekado

* 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





^ permalink raw reply	[flat|nested] 8+ messages in thread

* [bug#56999] [PATCH 2/4] gnu: Add phyml-mpi.
  2022-08-05  9:33 ` [bug#56999] [PATCH 1/4] gnu: Add phyml Mădălin Ionel Patrașcu
@ 2022-08-05  9:33   ` Mădălin Ionel Patrașcu
  2022-08-05  9:33   ` [bug#56999] [PATCH 3/4] gnu: Add phyml-phyrex Mădălin Ionel Patrașcu
                     ` (2 subsequent siblings)
  3 siblings, 0 replies; 8+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-08-05  9:33 UTC (permalink / raw)
  To: 56999; +Cc: rekado

* 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





^ permalink raw reply	[flat|nested] 8+ messages in thread

* [bug#56999] [PATCH 3/4] gnu: Add phyml-phyrex.
  2022-08-05  9:33 ` [bug#56999] [PATCH 1/4] gnu: Add phyml Mădălin Ionel Patrașcu
  2022-08-05  9:33   ` [bug#56999] [PATCH 2/4] gnu: Add phyml-mpi Mădălin Ionel Patrașcu
@ 2022-08-05  9:33   ` Mădălin Ionel Patrașcu
  2022-08-05  9:33   ` [bug#56999] [PATCH 4/4] nu: Add phyml-rf Mădălin Ionel Patrașcu
  2022-08-08  8:09   ` [bug#56999] [PATCH 1/4] gnu: Add phyml Ricardo Wurmus
  3 siblings, 0 replies; 8+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-08-05  9:33 UTC (permalink / raw)
  To: 56999; +Cc: rekado

* 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





^ permalink raw reply	[flat|nested] 8+ messages in thread

* [bug#56999] [PATCH 4/4] nu: Add phyml-rf.
  2022-08-05  9:33 ` [bug#56999] [PATCH 1/4] gnu: Add phyml Mădălin Ionel Patrașcu
  2022-08-05  9:33   ` [bug#56999] [PATCH 2/4] gnu: Add phyml-mpi Mădălin Ionel Patrașcu
  2022-08-05  9:33   ` [bug#56999] [PATCH 3/4] gnu: Add phyml-phyrex Mădălin Ionel Patrașcu
@ 2022-08-05  9:33   ` Mădălin Ionel Patrașcu
  2022-08-08  8:09   ` [bug#56999] [PATCH 1/4] gnu: Add phyml Ricardo Wurmus
  3 siblings, 0 replies; 8+ messages in thread
From: Mădălin Ionel Patrașcu @ 2022-08-05  9:33 UTC (permalink / raw)
  To: 56999; +Cc: rekado

* 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





^ permalink raw reply	[flat|nested] 8+ messages in thread

* [bug#56999] [PATCH 1/4] gnu: Add phyml.
  2022-08-05  9:33 ` [bug#56999] [PATCH 1/4] gnu: Add phyml Mădălin Ionel Patrașcu
                     ` (2 preceding siblings ...)
  2022-08-05  9:33   ` [bug#56999] [PATCH 4/4] nu: Add phyml-rf Mădălin Ionel Patrașcu
@ 2022-08-08  8:09   ` Ricardo Wurmus
  3 siblings, 0 replies; 8+ messages in thread
From: Ricardo Wurmus @ 2022-08-08  8:09 UTC (permalink / raw)
  To: Mădălin Ionel Patrașcu; +Cc: 56999


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




^ permalink raw reply	[flat|nested] 8+ messages in thread

* [bug#56999] [ext] bug#56999: Acknowledgement (Add phyml package tools.)
  2022-08-05  9:29   ` [bug#56999] [ext] bug#56999: Acknowledgement (Add phyml package tools.) MadalinIonel.Patrascu
@ 2022-08-08 10:35     ` Ricardo Wurmus
  0 siblings, 0 replies; 8+ messages in thread
From: Ricardo Wurmus @ 2022-08-08 10:35 UTC (permalink / raw)
  To: Patrascu, Madalin Ionel; +Cc: 56999-done@debbugs.gnu.org

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




^ permalink raw reply	[flat|nested] 8+ messages in thread

end of thread, other threads:[~2022-08-08 11:20 UTC | newest]

Thread overview: 8+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2022-08-05  9:14 [bug#56999] Add phyml package tools MadalinIonel.Patrascu
     [not found] ` <handler.56999.B.165969091927817.ack@debbugs.gnu.org>
2022-08-05  9:29   ` [bug#56999] [ext] bug#56999: Acknowledgement (Add phyml package tools.) MadalinIonel.Patrascu
2022-08-08 10:35     ` Ricardo Wurmus
2022-08-05  9:33 ` [bug#56999] [PATCH 1/4] gnu: Add phyml Mădălin Ionel Patrașcu
2022-08-05  9:33   ` [bug#56999] [PATCH 2/4] gnu: Add phyml-mpi Mădălin Ionel Patrașcu
2022-08-05  9:33   ` [bug#56999] [PATCH 3/4] gnu: Add phyml-phyrex Mădălin Ionel Patrașcu
2022-08-05  9:33   ` [bug#56999] [PATCH 4/4] nu: Add phyml-rf Mădălin Ionel Patrașcu
2022-08-08  8:09   ` [bug#56999] [PATCH 1/4] gnu: Add phyml Ricardo Wurmus

Code repositories for project(s) associated with this inbox:

	https://git.savannah.gnu.org/cgit/guix.git

This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).