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SPAdes GCC & Python versions #78

SPAdes GCC & Python versions

SPAdes GCC & Python versions #78

Workflow file for this run

name: SPAdes GCC & Python versions
on:
workflow_dispatch:
pull_request:
paths-ignore:
- 'docs/**'
- 'mkdocs.yml'
push:
tags:
- '*'
schedule:
- cron: '30 23 6,12,18,24,30 * *'
env:
BUILD_TYPE: Release
BUILD_DIR: ${{github.workspace}}/build
INSTALL_DIR: ${{github.workspace}}/spades
SRC_DIR: ${{github.workspace}}/src
PKG: SPAdes-*-Linux
jobs:
build-gcc9:
runs-on:
labels: [self-hosted, worker-1]
name: '🚧 Build SPAdes with GCC9'
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v4
with:
fetch-depth: 1
- name: 'βš™οΈ Install ccache'
uses: hendrikmuhs/[email protected]
with:
variant: sccache
key: sccache-${{env.BUILD_TYPE}}-gcc9
- name: 'βš™οΈ Configure CMake'
run: >
cmake
-B ${{env.BUILD_DIR}}
-S ${{env.SRC_DIR}}
-DCMAKE_C_COMPILER=gcc-9 -DCMAKE_CXX_COMPILER=g++-9
-DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
-DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}}
-DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC9-Linux
- name: '🚧 Build'
run: >
cmake
--build ${{env.BUILD_DIR}}
-j16
-t package
- name: 'πŸ“¦ Package'
uses: actions/upload-artifact@v4
with:
name: build-artifacts-gcc9
path: |
${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz
spades-test-python38:
name: 'E. coli 1k run with Python3.8'
runs-on:
labels: [self-hosted, worker-1]
needs: build-gcc9
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: 'πŸ“¦ Download package'
uses: actions/download-artifact@v4
with:
name: build-artifacts-gcc9
path: ${{env.INSTALL_DIR}}
- name: 'πŸ“¦ Unpack package'
working-directory: ${{env.INSTALL_DIR}}
run: >
tar -zxf ${{env.PKG}}.tar.gz
- name: 'E.coli 1K with Python 3.8'
run: >
python3.8 ${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test
build-gcc10:
runs-on:
labels: [self-hosted, worker-1]
name: '🚧 Build SPAdes with GCC10'
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v4
with:
fetch-depth: 1
- name: 'βš™οΈ Install ccache'
uses: hendrikmuhs/[email protected]
with:
variant: sccache
key: sccache-${{env.BUILD_TYPE}}-gcc10
- name: 'βš™οΈ Configure CMake'
run: >
cmake
-B ${{env.BUILD_DIR}}
-S ${{env.SRC_DIR}}
-DCMAKE_C_COMPILER=gcc-10 -DCMAKE_CXX_COMPILER=g++-10
-DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
-DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}}
-DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC10-Linux
- name: '🚧 Build'
run: >
cmake
--build ${{env.BUILD_DIR}}
-j16
-t package
- name: 'πŸ“¦ Package'
uses: actions/upload-artifact@v4
with:
name: build-artifacts-gcc10
path: |
${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz
spades-test-python39:
name: 'E. coli 1k run with Python3.9'
runs-on:
labels: [self-hosted, worker-1]
needs: build-gcc10
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: 'πŸ“¦ Download package'
uses: actions/download-artifact@v4
with:
name: build-artifacts-gcc10
path: ${{env.INSTALL_DIR}}
- name: 'πŸ“¦ Unpack package'
working-directory: ${{env.INSTALL_DIR}}
run: >
tar -zxf ${{env.PKG}}.tar.gz
- name: 'E.coli 1K SC with Python 3.9'
run: >
python3.9 ${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test --sc
build-gcc11:
runs-on:
labels: [self-hosted, worker-1]
name: '🚧 Build SPAdes with GCC11'
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v4
with:
fetch-depth: 1
- name: 'βš™οΈ Install ccache'
uses: hendrikmuhs/[email protected]
with:
variant: sccache
key: sccache-${{env.BUILD_TYPE}}-gcc11
- name: 'βš™οΈ Configure CMake'
run: >
cmake
-B ${{env.BUILD_DIR}}
-S ${{env.SRC_DIR}}
-DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
-DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
-DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}}
-DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC11-Linux
- name: '🚧 Build'
run: >
cmake
--build ${{env.BUILD_DIR}}
-j16
-t package
- name: 'πŸ“¦ Package'
uses: actions/upload-artifact@v4
with:
name: build-artifacts-gcc11
path: |
${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz
spades-test-python310:
name: 'E. coli 1k run with Python3.10'
runs-on:
labels: [self-hosted, worker-1]
needs: build-gcc11
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: 'πŸ“¦ Download package'
uses: actions/download-artifact@v4
with:
name: build-artifacts-gcc11
path: ${{env.INSTALL_DIR}}
- name: 'πŸ“¦ Unpack package'
working-directory: ${{env.INSTALL_DIR}}
run: >
tar -zxf ${{env.PKG}}.tar.gz
- name: 'E.coli 1K meta with Python 3.10'
run: >
python3.10 ${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test --meta
build-gcc12:
runs-on:
labels: [self-hosted, worker-1]
name: '🚧 Build SPAdes with GCC12'
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v4
with:
fetch-depth: 1
- name: 'βš™οΈ Install ccache'
uses: hendrikmuhs/[email protected]
with:
variant: sccache
key: sccache-${{env.BUILD_TYPE}}-gcc12
- name: 'βš™οΈ Configure CMake'
run: >
cmake
-B ${{env.BUILD_DIR}}
-S ${{env.SRC_DIR}}
-DCMAKE_C_COMPILER=/home/ubuntu/bin/gcc12/bin/gcc -DCMAKE_CXX_COMPILER=/home/ubuntu/bin/gcc12/bin/g++
-DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
-DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}}
-DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC12-Linux
- name: '🚧 Build'
run: >
cmake
--build ${{env.BUILD_DIR}}
-j16
-t package
- name: 'πŸ“¦ Package'
uses: actions/upload-artifact@v4
with:
name: build-artifacts-gcc12
path: |
${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz
spades-test-python311:
name: 'E. coli 1k run with Python3.11'
runs-on:
labels: [self-hosted, worker-1]
needs: build-gcc12
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: 'πŸ“¦ Download package'
uses: actions/download-artifact@v4
with:
name: build-artifacts-gcc12
path: ${{env.INSTALL_DIR}}
- name: 'πŸ“¦ Unpack package'
working-directory: ${{env.INSTALL_DIR}}
run: >
tar -zxf ${{env.PKG}}.tar.gz
- name: 'E.coli 1K RNA with Python 3.11'
run: >
python3.11 ${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test --rna
build-gcc13:
runs-on:
labels: [self-hosted, worker-1]
name: '🚧 Build SPAdes with GCC13'
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v4
with:
fetch-depth: 1
- name: 'βš™οΈ Install ccache'
uses: hendrikmuhs/[email protected]
with:
variant: sccache
key: sccache-${{env.BUILD_TYPE}}-gcc13
- name: 'βš™οΈ Configure CMake'
run: >
cmake
-B ${{env.BUILD_DIR}}
-S ${{env.SRC_DIR}}
-DCMAKE_C_COMPILER=/home/ubuntu/bin/gcc13/bin/gcc -DCMAKE_CXX_COMPILER=/home/ubuntu/bin/gcc13/bin/g++
-DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
-DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}}
-DCPACK_PACKAGE_FILE_NAME=SPAdes-GCC13-Linux
- name: '🚧 Build'
run: >
cmake
--build ${{env.BUILD_DIR}}
-j16
-t package
- name: 'πŸ“¦ Package'
uses: actions/upload-artifact@v4
with:
name: build-artifacts-gcc13
path: |
${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz
spades-test-python312:
name: 'E. coli 1k run with Python3.12'
runs-on:
labels: [self-hosted, worker-1]
needs: build-gcc13
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: 'πŸ“¦ Download package'
uses: actions/download-artifact@v4
with:
name: build-artifacts-gcc13
path: ${{env.INSTALL_DIR}}
- name: 'πŸ“¦ Unpack package'
working-directory: ${{env.INSTALL_DIR}}
run: >
tar -zxf ${{env.PKG}}.tar.gz
- name: 'E.coli 1K Isolate with Python 3.13'
run: >
python3.12 ${{env.INSTALL_DIR}}/${{env.PKG}}/bin/spades.py --test --isolate