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fixing openmp for os X
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glis-glis committed Nov 7, 2024

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1 parent 7047da1 commit 5adb356
Showing 2 changed files with 27 additions and 16 deletions.
15 changes: 10 additions & 5 deletions recipes/atlas/build.sh
Original file line number Diff line number Diff line change
@@ -1,9 +1,14 @@
#!/bin/bash

mkdir -p build
cd build
cmake .. -GNinja -DCONDA=ON -DCMAKE_CXX_COMPILER=${CXX} -DCMAKE_LIBRARY_PATH=${CONDA_PREFIX}/lib -DCMAKE_INCLUDE_PATH=${CONDA_PREFIX}/include
ninja
cmake . -GNinja \
-DCONDA=ON \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_CXX_COMPILER=${CXX} \
-DCMAKE_LIBRARY_PATH=${CONDA_PREFIX}/lib \
-DCMAKE_INCLUDE_PATH=${CONDA_PREFIX}/include

ninja || exit 1

mkdir -p ${PREFIX}/bin
cp atlas ${PREFIX}/bin
cp atlas ${PREFIX}/bin || exit 1
chmod +x ${PREFIX}/bin/atlas
28 changes: 17 additions & 11 deletions recipes/atlas/meta.yaml
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
{% set version = "2.0.0-rc.5" %}
{% set version = "2.0.0" %}

package:
package:
name: atlas
version: 2.0.0
version: {{ version }}

source:
url: https://bitbucket.org/wegmannlab/atlas/get/{{ version }}.tar.gz
url: https://bitbucket.org/wegmannlab/atlas/get/{{ version }}-rc.5.tar.gz
sha256: fabbde9a4af8053f748568c666fbf0210e318f7794bd8d8aed827d5da37314d5

build:
@@ -15,27 +15,32 @@ build:

requirements:
build:
- git
- {{ compiler('cxx') }}
- cmake
- git
- ninja
- {{ compiler('cxx') }}
- sysroot_linux-64 =2.17 # [linux]
host:
- armadillo
- fmt
- htslib
- lapack
- libgomp # [linux]
- llvm-openmp # [osx]
- nlohmann_json
- openblas
- openmp
- sysroot_linux-64 =2.17 # [linux]
- zlib
run:
- armadillo
- fmt
- htslib
- lapack
- libgomp # [linux]
- llvm-openmp # [osx]
- nlohmann_json
- openblas
- openmp
- sysroot_linux-64 =2.17 # [linux]
- zlib

test:
@@ -46,13 +51,14 @@ test:
- atlas GLF --bam ATLAS_simulations.bam
- atlas saf --glf ATLAS_simulations.glf.gz --fasta ATLAS_simulations.fasta
- atlas majorMinor --glf ATLAS_simulations.glf.gz

- rm ATLAS_* *.parameters saf.saf.* || exit 1

about:
home: https://atlaswiki.netlify.app
license: GPLv3
license: GPL3
summary: "ATLAS: Analysis Tools for Ancient and Low-depth Samples"

extra:
additional-platforms:
- linux-aarch64
- osx-arm64
- osx-arm64

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