SPAdes long-read tests #86
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name: SPAdes long-read tests | |
on: | |
workflow_dispatch: | |
pull_request: | |
paths-ignore: | |
- 'docs/**' | |
- 'mkdocs.yml' | |
push: | |
tags: | |
- '*' | |
schedule: | |
- cron: '0 23 * * 1,4' | |
env: | |
BUILD_TYPE: Release | |
BUILD_DIR: ${{github.workspace}}/build | |
INSTALL_DIR: ${{github.workspace}}/spades | |
SRC_DIR: ${{github.workspace}}/src | |
PKG: SPAdes-*-Linux | |
jobs: | |
build: | |
runs-on: self-hosted | |
name: 'π§ Build SPAdes' | |
steps: | |
- name: 'π§Ή Cleanup' | |
run: > | |
set -e && | |
shopt -s dotglob && | |
rm -rf * | |
- name: 'π§° Checkout' | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 1 | |
- name: 'βοΈ Install ccache' | |
uses: hendrikmuhs/ccache-action@v1.2 | |
with: | |
variant: sccache | |
key: sccache-${{env.BUILD_TYPE}} | |
- name: 'βοΈ 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: 'π§ Build' | |
run: > | |
cmake | |
--build ${{env.BUILD_DIR}} | |
-j16 | |
-t package | |
- name: 'π¦ Package' | |
uses: actions/upload-artifact@v4 | |
with: | |
name: build-artifacts | |
path: | | |
${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz | |
ctg-ecoli-is220: | |
name: 'Untrusted contigs E.coli is220' | |
runs-on: self-hosted | |
needs: build | |
steps: | |
- name: 'π§Ή Cleanup' | |
run: > | |
set -e && | |
shopt -s dotglob && | |
rm -rf * | |
- name: 'π§° Checkout' | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 1 | |
- name: 'π¦ Download package' | |
uses: actions/download-artifact@v4 | |
with: | |
name: build-artifacts | |
path: ${{env.INSTALL_DIR}} | |
- name: 'π¦ 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/spades_tests/CTG_E.coli_is220.info | |
ctg-geophsycobacter: | |
name: 'Untrustred contigs Geophsycobacter' | |
runs-on: self-hosted | |
needs: build | |
steps: | |
- name: 'π§Ή Cleanup' | |
run: > | |
set -e && | |
shopt -s dotglob && | |
rm -rf * | |
- name: 'π§° Checkout' | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 1 | |
- name: 'π¦ Download package' | |
uses: actions/download-artifact@v4 | |
with: | |
name: build-artifacts | |
path: ${{env.INSTALL_DIR}} | |
- name: 'π¦ 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/spades_tests/CTG_Geophsycobacter.info | |
pb-amirum: | |
name: 'PacBio A.mirum' | |
runs-on: self-hosted | |
needs: build | |
steps: | |
- name: 'π§Ή Cleanup' | |
run: > | |
set -e && | |
shopt -s dotglob && | |
rm -rf * | |
- name: 'π§° Checkout' | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 1 | |
- name: 'π¦ Download package' | |
uses: actions/download-artifact@v4 | |
with: | |
name: build-artifacts | |
path: ${{env.INSTALL_DIR}} | |
- name: 'π¦ 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/spades_tests/PB_A.mirum.info | |
pb-mruber: | |
name: 'PacBio M.ruber' | |
runs-on: self-hosted | |
needs: build | |
steps: | |
- name: 'π§Ή Cleanup' | |
run: > | |
set -e && | |
shopt -s dotglob && | |
rm -rf * | |
- name: 'π§° Checkout' | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 1 | |
- name: 'π¦ Download package' | |
uses: actions/download-artifact@v4 | |
with: | |
name: build-artifacts | |
path: ${{env.INSTALL_DIR}} | |
- name: 'π¦ 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/spades_tests/PB_M.ruber.info | |
pb-mp-amirum: | |
name: 'PacBio+Mate-pairs A.mirum' | |
runs-on: self-hosted | |
needs: build | |
steps: | |
- name: 'π§Ή Cleanup' | |
run: > | |
set -e && | |
shopt -s dotglob && | |
rm -rf * | |
- name: 'π§° Checkout' | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 1 | |
- name: 'π¦ Download package' | |
uses: actions/download-artifact@v4 | |
with: | |
name: build-artifacts | |
path: ${{env.INSTALL_DIR}} | |
- name: 'π¦ 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/spades_tests/PB_MP_A.mirum.info | |
pb-mp-mruber: | |
name: 'PacBio+Mate-pairs M.ruber' | |
runs-on: self-hosted | |
needs: build | |
steps: | |
- name: 'π§Ή Cleanup' | |
run: > | |
set -e && | |
shopt -s dotglob && | |
rm -rf * | |
- name: 'π§° Checkout' | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 1 | |
- name: 'π¦ Download package' | |
uses: actions/download-artifact@v4 | |
with: | |
name: build-artifacts | |
path: ${{env.INSTALL_DIR}} | |
- name: 'π¦ 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/spades_tests/PB_MP_M.ruber.info | |
pb-ecoli: | |
name: 'PacBio P4 E.coli is200' | |
runs-on: self-hosted | |
needs: build | |
steps: | |
- name: 'π§Ή Cleanup' | |
run: > | |
set -e && | |
shopt -s dotglob && | |
rm -rf * | |
- name: 'π§° Checkout' | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 1 | |
- name: 'π¦ Download package' | |
uses: actions/download-artifact@v4 | |
with: | |
name: build-artifacts | |
path: ${{env.INSTALL_DIR}} | |
- name: 'π¦ 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/spades_tests/PB_P4_E.coli_is220.info | |
pb-pheparinus: | |
name: 'PacBio P.heparinus' | |
runs-on: self-hosted | |
needs: build | |
steps: | |
- name: 'π§Ή Cleanup' | |
run: > | |
set -e && | |
shopt -s dotglob && | |
rm -rf * | |
- name: 'π§° Checkout' | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 1 | |
- name: 'π¦ Download package' | |
uses: actions/download-artifact@v4 | |
with: | |
name: build-artifacts | |
path: ${{env.INSTALL_DIR}} | |
- name: 'π¦ 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/spades_tests/PB_P.heparinus.info | |
tctg-kpneumoniae: | |
name: 'Trusted contigs K.pneumoniae' | |
runs-on: self-hosted | |
needs: build | |
steps: | |
- name: 'π§Ή Cleanup' | |
run: > | |
set -e && | |
shopt -s dotglob && | |
rm -rf * | |
- name: 'π§° Checkout' | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 1 | |
- name: 'π¦ Download package' | |
uses: actions/download-artifact@v4 | |
with: | |
name: build-artifacts | |
path: ${{env.INSTALL_DIR}} | |
- name: 'π¦ 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/spades_tests/TCTG_K.pneumoniae.info | |
tctg-pstipitis: | |
name: 'Trusted contigs P.stipitis' | |
runs-on: self-hosted | |
needs: build | |
steps: | |
- name: 'π§Ή Cleanup' | |
run: > | |
set -e && | |
shopt -s dotglob && | |
rm -rf * | |
- name: 'π§° Checkout' | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 1 | |
- name: 'π¦ Download package' | |
uses: actions/download-artifact@v4 | |
with: | |
name: build-artifacts | |
path: ${{env.INSTALL_DIR}} | |
- name: 'π¦ 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/spades_tests/TCTG_P.stipitis.info | |
tctg-ssmaragdinae: | |
name: 'Trusted contigs S.smaragdinae quaked' | |
runs-on: self-hosted | |
needs: build | |
steps: | |
- name: 'π§Ή Cleanup' | |
run: > | |
set -e && | |
shopt -s dotglob && | |
rm -rf * | |
- name: 'π§° Checkout' | |
uses: actions/checkout@v4 | |
with: | |
fetch-depth: 1 | |
- name: 'π¦ Download package' | |
uses: actions/download-artifact@v4 | |
with: | |
name: build-artifacts | |
path: ${{env.INSTALL_DIR}} | |
- name: 'π¦ 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/spades_tests/TCTG_S.smaragdinae_quake.info | |