Skip to content
Update all SPAdes saves

Update all SPAdes saves #1

Sign in to view logs

Update all SPAdes saves

Update all SPAdes saves #1

Workflow file for this run

.github/workflows/update_saves.yml at cba71b7
name: Update all SPAdes saves
on:
workflow_dispatch:
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
- 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}}
key: sccache-${{env.BUILD_TYPE}}
- 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
run-saves-ecoli-100k:
name: 'Run saves E.coli 100K'
runs-on:
labels: [self-hosted, worker-1]
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 --no_cleanup --ignore_checks
/data/pipeline_tests/Saves_E.coli_100K.info
run-saves-ecoli-ucsd-lane1:
name: 'Run saves E.coli UCSD lane 1'
runs-on:
labels: [self-hosted, worker-1]
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 --no_cleanup --ignore_checks
/data/pipeline_tests/Saves_E.coli_UCSD_lane1.info
run-meta-ecoli-mix-saves:
name: 'Run E.coli mix saves'
runs-on:
labels: [self-hosted, worker-1]
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 --no_cleanup --ignore_checks
/data/meta_tests/ECOLI_MIX_SAVES.info
copy-saves:
runs-on:
labels: [self-hosted, worker-1]
name: '💾️ Copy saves'
needs: [run-saves-ecoli-100k, run-saves-ecoli-ucsd-lane1, run-meta-ecoli-mix-saves]
steps:
- name: 'E.coli 100K'
run: >
python3 ${{env.SRC_DIR}}/test/teamcity/update_saves.py
--saves_dir /data/pipeline_tests/etalon/ECOLI_IS220_100K
--output_dir /scratch/spades_output/ECOLI_100K/
- name: 'E.coli UCSD lane 1'
run: >
python3 ${{env.SRC_DIR}}/test/teamcity/update_saves.py
--saves_dir /data/pipeline_tests/etalon/SAVES_ECOLI_UCSD_L1
--output_dir /scratch/spades_output/SAVES_ECOLI_UCSD_L1/
- name: 'Meta E.coli UCSD lane 1'
run: >
python3 ${{env.SRC_DIR}}/test/teamcity/update_saves.py
--saves_dir /data/meta_tests/etalon/ECOLI_MIX_SAVES
--output_dir /scratch/meta_output/ECOLI_MIX_SAVES/
- name: '🧹 Cleanup'
run: >
set -e &&
rm -rf /scratch/spades_output/ECOLI_100K/K* &&
rm -rf /scratch/spades_output/SAVES_ECOLI_UCSD_L1/K* &&
rm -rf /scratch/meta_output/ECOLI_MIX_SAVES/K*
check-saves-ecoli-100k:
name: 'Check saves E.coli 100K'
runs-on: self-hosted
needs: [build, copy-saves]
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/pipeline_tests/Saves_E.coli_100K.info
check-saves-ecoli-ucsd-lane1:
name: 'Check saves E.coli UCSD lane 1'
runs-on: self-hosted
needs: [build, copy-saves]
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/pipeline_tests/Saves_E.coli_UCSD_lane1.info
check-meta-ecoli-mix-saves:
name: 'Check E.coli mix saves'
runs-on: self-hosted
needs: [build, copy-saves]
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/meta_tests/ECOLI_MIX_SAVES.info