Fix for package managers storing files in read-only #47

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: '⚙️ Install ccache'
	uses: hendrikmuhs/[email protected]
	with:
	variant: sccache
	key: sccache-${{env.BUILD_TYPE}}-gcc9

	- name: '⚙️ 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: '📦 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: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts-gcc9
	path: ${{env.INSTALL_DIR}}
	- name: '📦 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: '⚙️ Install ccache'
	uses: hendrikmuhs/[email protected]
	with:
	variant: sccache
	key: sccache-${{env.BUILD_TYPE}}-gcc10

	- name: '⚙️ 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: '📦 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: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts-gcc10
	path: ${{env.INSTALL_DIR}}
	- name: '📦 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: '⚙️ Install ccache'
	uses: hendrikmuhs/[email protected]
	with:
	variant: sccache
	key: sccache-${{env.BUILD_TYPE}}-gcc11

	- name: '⚙️ 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: '📦 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: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts-gcc11
	path: ${{env.INSTALL_DIR}}
	- name: '📦 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: '⚙️ Install ccache'
	uses: hendrikmuhs/[email protected]
	with:
	variant: sccache
	key: sccache-${{env.BUILD_TYPE}}-gcc12

	- name: '⚙️ 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: '📦 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: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts-gcc12
	path: ${{env.INSTALL_DIR}}
	- name: '📦 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: '⚙️ Install ccache'
	uses: hendrikmuhs/[email protected]
	with:
	variant: sccache
	key: sccache-${{env.BUILD_TYPE}}-gcc13

	- name: '⚙️ 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: '📦 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: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts-gcc13
	path: ${{env.INSTALL_DIR}}
	- name: '📦 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

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Fix for package managers storing files in read-only #47

Workflow file

Fix for package managers storing files in read-only #47

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Workflow file for this run