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SPAdes long-read tests

SPAdes long-read tests #410

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SPAdes long-read tests

SPAdes long-read tests #410

Workflow file for this run

.github/workflows/long_reads.yml at 808b87d
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: ${{github.workspace}}/src
PKG: SPAdes-*-Linux
jobs:
build:
runs-on: self-hosted
name: '🚧 Build SPAdes'
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v4
with:
fetch-depth: 1
- name: '⚙️ Install ccache'
uses: hendrikmuhs/ccache-action@v1.2
with:
variant: sccache
key: sccache-${{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
ctg-ecoli-is220:
name: 'Untrusted contigs E.coli is220'
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/spades_tests/CTG_E.coli_is220.info
ctg-geophsycobacter:
name: 'Untrustred contigs Geophsycobacter'
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/spades_tests/CTG_Geophsycobacter.info
pb-amirum:
name: 'PacBio A.mirum'
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/spades_tests/PB_A.mirum.info
pb-mruber:
name: 'PacBio M.ruber'
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/spades_tests/PB_M.ruber.info
pb-mp-amirum:
name: 'PacBio+Mate-pairs A.mirum'
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/spades_tests/PB_MP_A.mirum.info
pb-mp-mruber:
name: 'PacBio+Mate-pairs M.ruber'
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/spades_tests/PB_MP_M.ruber.info
pb-ecoli:
name: 'PacBio P4 E.coli is200'
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/spades_tests/PB_P4_E.coli_is220.info
pb-pheparinus:
name: 'PacBio P.heparinus'
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/spades_tests/PB_P.heparinus.info
tctg-kpneumoniae:
name: 'Trusted contigs K.pneumoniae'
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/spades_tests/TCTG_K.pneumoniae.info
tctg-pstipitis:
name: 'Trusted contigs P.stipitis'
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/spades_tests/TCTG_P.stipitis.info
tctg-ssmaragdinae:
name: 'Trusted contigs S.smaragdinae quaked'
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/spades_tests/TCTG_S.smaragdinae_quake.info