[DO NOT MERGE] hpcSPAdes rebase, cleanup & implementation #103

Workflow file for this run

	name: metaSPAdes tests

	on:
	workflow_dispatch:
	pull_request:
	paths-ignore:
	- 'docs/**'
	- 'mkdocs.yml'
	push:
	tags:
	- '*'
	schedule:
	- cron: '0 22 * * 2,5'

	env:
	BUILD_TYPE: Release
	BUILD_DIR: ${{github.workspace}}/build
	INSTALL_DIR: ${{github.workspace}}/spades
	SRC_DIR: ${{github.workspace}}/src
	PKG: SPAdes-*-Linux

	jobs:
	build:
	runs-on: self-hosted
	name: '🚧 Build SPAdes'

	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}}

	- name: '⚙️ Configure CMake'
	run: >
	cmake
	-B ${{env.BUILD_DIR}}
	-S ${{env.SRC_DIR}}
	-DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
	-DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}}

	- name: '🚧 Build'
	run: >
	cmake
	--build ${{env.BUILD_DIR}}
	-j16
	-t package

	- name: '📦 Package'
	uses: actions/upload-artifact@v4
	with:
	name: build-artifacts
	path: \|
	${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz

	meta-ecoli-mix-saves:
	name: 'E.coli mix saves'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/meta_tests/ECOLI_MIX_SAVES.info

	meta-hmp-mock-full:
	name: 'HMP staggered Mock full'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/meta_tests/HMP_STAGGERED_MOCK_FULL.info

	meta-mbarc-26-150:
	name: 'MBARC 25 150'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/meta_tests/MBARC_26_150.info

	meta-mbarc-26-150-interlaced:
	name: 'MBARC 25 150 interlaced'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/meta_tests/MBARC_26_150_interlaced.info

	meta-mbarc-26-250:
	name: 'MBARC 25 250'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/meta_tests/MBARC_26_250.info

	meta-mc-bcereus-truseq-100x:
	name: 'Multi-cell B.cereus TruSeq 100x'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/meta_tests/MC_BCEREUS_TRUSEQ_100x.info

	meta-synth64-sub-0p2:
	name: 'Synth64 Sub 0p2'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/meta_tests/SYNTH_64_SUB_0p2.info

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

[DO NOT MERGE] hpcSPAdes rebase, cleanup & implementation #103

Workflow file

[DO NOT MERGE] hpcSPAdes rebase, cleanup & implementation #103

Jobs

Run details

Workflow file for this run