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Workflow file for this run

name: SPAdes single-cell datasets tests
on:
workflow_dispatch:
pull_request:
push:
tags:
- '*'
schedule:
- cron: '0 12 * * 2,6'
env:
BUILD_TYPE: Release
BUILD_DIR: ${{github.workspace}}/build
INSTALL_DIR: ${{github.workspace}}/spades
SRC_DIR: ${{github.workspace}}/src
PKG: SPAdes-*-Linux
jobs:
build:
runs-on: self-hosted
name: '🚧 Build SPAdes'
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v3
with:
fetch-depth: 1
- name: '⚙️ Install ccache'
uses: hendrikmuhs/[email protected]
with:
variant: sccache
key: sccache-${{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@v3
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: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v3
with:
fetch-depth: 1
- name: '📦 Download package'
uses: actions/download-artifact@v3
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/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: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v3
with:
fetch-depth: 1
- name: '📦 Download package'
uses: actions/download-artifact@v3
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/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: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v3
with:
fetch-depth: 1
- name: '📦 Download package'
uses: actions/download-artifact@v3
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/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: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v3
with:
fetch-depth: 1
- name: '📦 Download package'
uses: actions/download-artifact@v3
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/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: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v3
with:
fetch-depth: 1
- name: '📦 Download package'
uses: actions/download-artifact@v3
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/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: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v3
with:
fetch-depth: 1
- name: '📦 Download package'
uses: actions/download-artifact@v3
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/spades_tests/SC_M.ruber_JGI_lane9.info
sc-pmarinus:
name: 'Single-cell P.marinus'
runs-on: self-hosted
needs: build
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v3
with:
fetch-depth: 1
- name: '📦 Download package'
uses: actions/download-artifact@v3
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/spades_tests/SC_P.marinus.info
sc-pb-tm6:
name: 'Single-cell+PacBio TM6'
runs-on: self-hosted
needs: build
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v3
with:
fetch-depth: 1
- name: '📦 Download package'
uses: actions/download-artifact@v3
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/spades_tests/SC_PB_Tm6.info
sc-se-pmarinus:
name: 'Single-cell single-end P.marinus'
runs-on: self-hosted
needs: build
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v3
with:
fetch-depth: 1
- name: '📦 Download package'
uses: actions/download-artifact@v3
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/spades_tests/SC_SE_P.marinus.info