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iqtree: new port, version 1.6.12

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ttung authored and reneeotten committed May 14, 2020
1 parent ca1379d commit 97ae5d816f800e429f56e63e75824f70b8ab5a1f
Showing with 72 additions and 0 deletions.
  1. +47 −0 science/iqtree/Portfile
  2. +25 −0 science/iqtree/files/patch-CMakeLists.txt.diff
@@ -0,0 +1,47 @@
# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4

PortSystem 1.0
PortGroup github 1.0
PortGroup cmake 1.1

github.setup Cibiv IQ-TREE 1.6.12 v
github.tarball_from archive
name iqtree
revision 0

categories science
platforms darwin
license GPL-2
maintainers nomaintainer

description Efficient phylogenomic software by maximum likelihood
long_description The IQ-TREE software was created as the successor of IQPNNI and \
TREE-PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the \
rapid accumulation of phylogenomic data, leading to a need for \
efficient phylogenomic software that can handle a large amount of \
data and provide more complex models of sequence evolution. To this \
end, IQ-TREE can utilize multicore computers and distributed parallel \
computing to speed up the analysis. IQ-TREE automatically performs \
checkpointing to resume an interrupted analysis.

homepage http://www.iqtree.org/

checksums rmd160 249414b567bc4f3d2a939d8f7e71cd72f653ed3c \
sha256 9614092de7a157de82c9cc402b19cc8bfa0cb0ffc93b91817875c2b4bb46a284 \
size 4864641

patchfiles-append patch-CMakeLists.txt.diff

depends_build-append port:eigen3 \
port:libomp \
port:zlib

compiler.cxx_standard 2011
compiler.cpath-append ${prefix}/include/libomp

post-destroot {
xinstall -d ${destroot}${prefix}/share/doc/${name}
foreach file {example.nex example.cf models.nex example.phy} {
move ${destroot}${prefix}/${file} ${destroot}${prefix}/share/doc/${name}
}
}
@@ -0,0 +1,25 @@
--- CMakeLists.txt.orig 2020-06-06 10:59:21.000000000 -0400
+++ CMakeLists.txt 2020-06-06 11:01:08.000000000 -0400
@@ -89,14 +89,14 @@
add_definitions(-DWIN32)
elseif (APPLE)
message("Target OS : Mac OS X")
- # to be compatible back to Mac OS X 10.7
- if (IQTREE_FLAGS MATCHES "oldmac")
- add_definitions("-mmacosx-version-min=10.5")
- set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -mmacosx-version-min=10.5")
- else()
- add_definitions("-mmacosx-version-min=10.7")
- set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -mmacosx-version-min=10.7")
- endif()
+ ## # to be compatible back to Mac OS X 10.7
+ ## if (IQTREE_FLAGS MATCHES "oldmac")
+ ## add_definitions("-mmacosx-version-min=10.5")
+ ## set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -mmacosx-version-min=10.5")
+ ## else()
+ ## add_definitions("-mmacosx-version-min=10.7")
+ ## set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -mmacosx-version-min=10.7")
+ ## endif()

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@ryandesign

ryandesign Jun 12, 2020

Contributor

In the future, please don't write patchfiles that comment out lines. Instead, write patchfiles that remove lines. This makes the patchfiles smaller and easier to read.

SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
elseif (UNIX)
message("Target OS : Unix")

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