SPAdes single-cell datasets tests #87
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name: SPAdes single-cell datasets tests | |
on: | |
workflow_dispatch: | |
pull_request: | |
paths-ignore: | |
- 'docs/**' | |
- 'mkdocs.yml' | |
push: | |
tags: | |
- '*' | |
schedule: | |
- cron: '0 12 * * 2,6' | |
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 | |
sc-ecoli-deeptrench: | |
name: 'Single-cell E.coli deeptrench' | |
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/SC_E.coli_deeptrench.info | |
sc-ecoli-jgi-lane7: | |
name: 'Single-cell E.coli JGI lane 7' | |
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/SC_E.coli_JGI_lane7.info | |
sc-ecoli-jgi-lane7-2libs: | |
name: 'Single-cell E.coli JGI lane 7 2 libraries' | |
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/SC_E.coli_JGI_lane7_2lib.info | |
sc-ctg-ecoli-ucsd-lane1: | |
name: 'Single-cell+contigs E.coli UCSD lane 1' | |
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/SC_CGT_E.coli_UCSD_lane1.info | |
sc-pheparinus-jgi-lane7: | |
name: 'Single-cell P.heparinus JGI lane 7' | |
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/SC_P.heparinus_JGI_lane7.info | |
sc-mruber-jgi-lane9: | |
name: 'Single-cell M.ruber JGI lane 9' | |
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/SC_M.ruber_JGI_lane9.info | |
sc-pmarinus: | |
name: 'Single-cell P.marinus' | |
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/SC_P.marinus.info | |
sc-pb-tm6: | |
name: 'Single-cell+PacBio TM6' | |
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/SC_PB_Tm6.info | |
sc-se-pmarinus: | |
name: 'Single-cell single-end P.marinus' | |
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/SC_SE_P.marinus.info |