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Update freebayes recipe (bioconda#46882)
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* Update freebayes recipe

* add zlib back to run

* edit build.sh

* add macos patch

* add build selector
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mencian authored Mar 29, 2024
1 parent 2b37972 commit 8c95e97
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Showing 4 changed files with 21 additions and 26 deletions.
13 changes: 13 additions & 0 deletions recipes/freebayes/0003-meson-macos.patch
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
diff --git a/meson.build b/meson.build
index 66b8016..bf0bf10 100644
--- a/meson.build
+++ b/meson.build
@@ -16,7 +16,7 @@

project('freebayes', ['cpp', 'c'],
version : '1.3.7',
- default_options : ['warning_level=1', 'cpp_std=c++17', 'optimization=3'])
+ default_options : ['warning_level=1', 'cpp_std=c++14', 'optimization=3'])
static_build = get_option('static')

cc = meson.get_compiler('cpp')
19 changes: 0 additions & 19 deletions recipes/freebayes/LICENSE

This file was deleted.

8 changes: 4 additions & 4 deletions recipes/freebayes/build.sh
Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
#!/bin/bash

mkdir build
meson setup --buildtype debug --prefix "${PREFIX}" -Dprefer_system_deps=true build/

mkdir -p ${PREFIX}/bin

CXX="${CXX}" CC="${CC}" meson setup --buildtype release --prefix "${PREFIX}" \
--strip --prefer-static -Dprefer_system_deps=true build/

cd build
ninja -v
Expand All @@ -13,7 +14,6 @@ ninja -v install
##Copy scripts over ## This will likely need to be removed with an updated build
cp -n ../scripts/*.py $PREFIX/bin
cp -n ../scripts/*.sh $PREFIX/bin
cp -n ../scripts/*.pl $PREFIX/bin
#cp -n ../scripts/*.R $PREFIX/bin
cp -n ../scripts/*.pl $PREFIX/bin

cp -n ../scripts/freebayes-parallel $PREFIX/bin
7 changes: 4 additions & 3 deletions recipes/freebayes/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
{% set name = "freebayes" %}
{% set version = "1.3.7" %}

package:
name: freebayes
name: {{ name }}
version: {{ version }}

source:
Expand All @@ -10,10 +11,10 @@ source:
patches:
- 0001-make-meson-build-conda-friendly.patch
- 0002-fix-intervaltree-include-path.patch
- 0003-meson-macos.patch # [osx]

build:
number: 1
skip: true # [osx]
number: 2
run_exports:
- {{ pin_subpackage("freebayes", max_pin="x") }}

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