Add PhyML (#5033)

* Add PhyML * Add PhyML 3.2.0 * Pin openmpi to 2.* * Pin beagle-lib to >=2.1.2-7 For some odd reason, the test stage likes to install other package versions, like in this case the 2.1.2-1 which has different requirements (doesn't need libtool), leading to linking failure. * Pinning to build numbers doesn't seem to work? * Add missing patch
bioconda · Jun 24, 2017 · 6725096 · 6725096
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diff --git a/recipes/phyml/3.2.0/build.sh b/recipes/phyml/3.2.0/build.sh
@@ -0,0 +1,28 @@
+#!/bin/bash
+set -x
+set +e
+
+sh autogen.sh
+
+# PhyML builds different binaries depending on configure flags.
+# We build
+#   - phyml (enable-phyml),
+#   - phyml-mpi (enable-mpi),
+#   - phytime
+# but not
+#   - phyml-beagle -- doesn't compile in this relase
+#   - phyrex -- doesn't build
+
+for binary in beagle mpi phyml; do
+    ./configure \
+	--disable-dependency-tracking \
+	--prefix $PREFIX \
+	--disable-debug \
+	--enable-$binary
+    make -j$CPU_COUNT
+    make check
+    make install
+    make clean
+done
+
+
diff --git a/recipes/phyml/3.2.0/meta.yaml b/recipes/phyml/3.2.0/meta.yaml
@@ -0,0 +1,67 @@
+{% set name = "PhyML" %}
+{% set version = "3.2.0" %}
+{% set sha256 = "9fec8fc26e69cad8d58bf2c9433b531754e4f026dc3464d07958b6c824783fde" %}
+
+package:
+  name: {{ name | lower }}
+  version: {{ version }}
+
+source:
+  fn: {{ name | lower }}-{{ version }}.tar.gz
+  url: https://github.com/stephaneguindon/{{ name | lower }}/archive/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+  patches:
+    # don't update version to current date
+    - pin_version.patch
+
+build:
+  number: 0
+
+requirements:
+  build:
+    - gcc   # [linux]
+    - llvm  # [osx]
+    - autoconf
+    - automake
+    - pkg-config
+    - openmpi 2.*
+    - beagle-lib
+    - libtool
+  run:
+    - libgcc   # [linux]
+    - openmpi 2.*
+    - beagle-lib
+    - libtool
+test:
+  requirements:
+    - conda
+  commands:
+    # conda isn't always installed in the test env, wrap with if to get failure
+    # only if conda is there and inspect fails
+    - if command -v conda; then conda inspect linkages -p $PREFIX $PKG_NAME; fi
+    - if command -v conda; then conda inspect objects -p $PREFIX $PKG_NAME; fi # [osx]
+    - phyml --help | grep "PhyML {{ version }}"
+    # mpirun flags needed to work around docker image:
+    #   - runs as root (--allow-run-as-root)
+    #   - doesn't have rsh or ssh (-mca orte_rsh_agent /bin/true)
+    - mpirun -mca orte_rsh_agent true --allow-run-as-root phyml-mpi --help | grep "PhyML {{ version }}"
+    - phyml-beagle --help | grep "PhyML {{ version }}"
+
+about:
+  home: http://www.atgc-montpellier.fr/phyml/
+  dev_url: https://github.com/stephaneguindon/phyml/
+  license: GPLv2
+  license_family: GPL
+  license_file: COPYING
+  summary: Phylogenetic estimation using (Maximum) Likelihood 
+  description: |
+    PhyML is a software that estimates maximum likelihood phylogenies from
+    alignments of nucleotide or amino acid sequences. The main strength of
+    PhyML lies in the large number of substitution models coupled to various
+    options to search the space of phylogenetic tree topologies, going from
+    very fast and efficient methods to slower but generally more accurate
+    approaches. PhyML was designed to process moderate to large data sets. In
+    theory, alignments with up to 4,000 sequences 2,000,000 character-long
+    can be processed. PhyML can process data sets made of multiple genes and
+    fit sophisticated substitution models with heterogeneous components
+    across partition elements.
diff --git a/recipes/phyml/3.2.0/pin_version.patch b/recipes/phyml/3.2.0/pin_version.patch
@@ -0,0 +1,13 @@
+diff -ru phyml-3.3.20170530.orig/configure.ac phyml-3.3.20170530/configure.ac
+--- phyml-3.3.20170530.orig/configure.ac	2017-05-23 00:38:26.000000000 -0600
++++ phyml-3.3.20170530/configure.ac	2017-06-22 13:30:43.000000000 -0600
+@@ -1,7 +1,8 @@
+ #                                               -*- Autoconf -*-
+ # Process this file with autoconf to produce a configure script.
+
+-AC_INIT([PhyML],esyscmd([sh -c "date \"+%Y%m%d\" | tr -d '\n'"]),[s.guindon@auckland.ac.nz])
++dnl AC_INIT([PhyML],esyscmd([sh -c "date \"+%Y%m%d\" | tr -d '\n'"]),[s.guindon@auckland.ac.nz])
++AC_INIT([PhyML],[3.2.0],[s.guindon@auckland.ac.nz])
+ AM_INIT_AUTOMAKE([foreign])
+ m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES])
+ AC_CONFIG_MACRO_DIR([m4])
diff --git a/recipes/phyml/build.sh b/recipes/phyml/build.sh
@@ -0,0 +1,28 @@
+#!/bin/bash
+set -x
+set +e
+
+sh autogen.sh
+
+# PhyML builds different binaries depending on configure flags.
+# We build
+#   - phyml (enable-phyml),
+#   - phyml-mpi (enable-mpi),
+#   - phytime
+# but not
+#   - phyml-beagle -- doesn't compile in this relase
+#   - phyrex -- crashes with segfault
+
+for binary in mpi phyml phyrex phytime; do
+    ./configure \
+	--disable-dependency-tracking \
+	--prefix $PREFIX \
+	--disable-debug \
+	--enable-$binary
+    make -j$CPU_COUNT
+    make check
+    make install
+    make clean
+done
+
+
diff --git a/recipes/phyml/meta.yaml b/recipes/phyml/meta.yaml
@@ -0,0 +1,67 @@
+{% set name = "PhyML" %}
+{% set version = "3.3.20170530" %}
+{% set sha256 = "f826726cd56b755be75f923abdf29aca8a9951d6af948cddbab40739a8f99f74" %}
+
+package:
+  name: {{ name | lower }}
+  version: {{ version }}
+
+source:
+  fn: {{ name | lower }}-{{ version }}.tar.gz
+  url: https://github.com/stephaneguindon/{{ name | lower }}/archive/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+  patches:
+    # remove broken include
+    - no_malloc_h.patch
+    # don't update version to current date
+    - pin_version.patch
+
+build:
+  number: 0
+
+requirements:
+  build:
+    - gcc   # [linux]
+    - llvm  # [osx]
+    - autoconf
+    - automake
+    - pkg-config
+    - openmpi 2.*
+    - beagle-lib
+  run:
+    - libgcc   # [linux]
+    - openmpi 2.*
+    - beagle-lib
+test:
+  requirements:
+    - conda
+  commands:
+    # conda isn't always installed in the test env, wrap with if to get failure
+    # only if conda is there and inspect fails
+    - if command -v conda; then conda inspect linkages -p $PREFIX $PKG_NAME; fi
+    - if command -v conda; then conda inspect objects -p $PREFIX $PKG_NAME; fi # [osx]
+    - phyml --help | grep "PhyML {{ version }}"
+    # mpirun flags needed to work around docker image:
+    #   - runs as root (--allow-run-as-root)
+    #   - doesn't have rsh or ssh (-mca orte_rsh_agent /bin/true)
+    - mpirun -mca orte_rsh_agent true --allow-run-as-root phyml-mpi --help | grep "PhyML {{ version }}"
+    - phytime --help | grep "PhyTime {{ version }}"
+
+about:
+  home: http://www.atgc-montpellier.fr/phyml/
+  dev_url: https://github.com/stephaneguindon/phyml/
+  license: GPLv2
+  license_family: GPL
+  license_file: COPYING
+  summary: Phylogenetic estimation using (Maximum) Likelihood 
+  description: |
+    PhyML is a software that estimates maximum likelihood phylogenies from
+    alignments of nucleotide or amino acid sequences. The main strength of
+    PhyML lies in the large number of substitution models coupled to various
+    options to search the space of phylogenetic tree topologies, going from
+    very fast and efficient methods to slower but generally more accurate
+    approaches. PhyML was designed to process moderate to large data sets. In
+    theory, alignments with up to 4,000 sequences 2,000,000 character-long
+    can be processed. PhyML can process data sets made of multiple genes and
+    fit sophisticated substitution models with heterogeneous components
+    across partition elements.
diff --git a/recipes/phyml/no_malloc_h.patch b/recipes/phyml/no_malloc_h.patch
@@ -0,0 +1,12 @@
+diff -ur phyml-3.3.20170530.orig/src/utilities.h phyml-3.3.20170530/src/utilities.h
+--- phyml-3.3.20170530.orig/src/utilities.h	2017-05-23 00:38:26.000000000 -0600
++++ phyml-3.3.20170530/src/utilities.h	2017-06-21 17:49:32.000000000 -0600
+@@ -28,8 +28,6 @@
+ #include <float.h>
+ #include <assert.h>
+ #include <stdbool.h>
+-/* #include <malloc/malloc.h> */
+-#include <malloc.h>
+
+ #if (defined(__AVX__))
+ #include <xmmintrin.h>
diff --git a/recipes/phyml/pin_version.patch b/recipes/phyml/pin_version.patch
@@ -0,0 +1,13 @@
+diff -ru phyml-3.3.20170530.orig/configure.ac phyml-3.3.20170530/configure.ac
+--- phyml-3.3.20170530.orig/configure.ac	2017-05-23 00:38:26.000000000 -0600
++++ phyml-3.3.20170530/configure.ac	2017-06-22 13:30:43.000000000 -0600
+@@ -1,7 +1,8 @@
+ #                                               -*- Autoconf -*-
+ # Process this file with autoconf to produce a configure script.
+
+-AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; date \"+%Y%m%d\" | tr -d '\n'"]),[guindon@lirmm.fr])
++dnl AC_INIT([PhyML],esyscmd([sh -c "echo "3.3." | tr -d '\n' ; date \"+%Y%m%d\" | tr -d '\n'"]),[guindon@lirmm.fr])
++AC_INIT([PhyML],[3.3.20170530],[guindon@lirmm.fr])
+ AM_INIT_AUTOMAKE([foreign])
+ m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES])
+ AC_CONFIG_MACRO_DIR([m4])