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update readme, remove old html mans #9

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update readme, remove old html mans

update readme, remove old html mans #9

Workflow file for this run

.github/workflows/usecases.yml at 5b7de16
name: SPAdes usecases
on:
workflow_dispatch:
push:
branches:
- master
- main
- next
tags:
- '*'
pull_request:
env:
BUILD_TYPE: Release
BUILD_DIR: ${{github.workspace}}/build
INSTALL_DIR: ${{github.workspace}}/spades
SRC_DIR: ${{github.workspace}}/src
PKG: SPAdes-*-Linux
jobs:
build:
runs-on: self-hosted
name: '🚧 Build SPAdes'
steps:
- name: '🧹 Cleanup'
run: >
set -e &&
shopt -s dotglob &&
rm -rf *
- name: '🧰 Checkout'
uses: actions/checkout@v3
with:
fetch-depth: 1
- name: '⚙️ Install ccache'
uses: hendrikmuhs/ccache-action@v1.2
with:
variant: sccache
key: sccache-${{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@v3
with:
name: build-artifacts
path: |
${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz
mc-bcereus-truseq-100x:
name: 'Multicell B.cereus TruSeq 100x'
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/pipeline_tests/Multicell_B.cereus_TruSeq_100x.info
nextera-lmonocytogenes:
name: 'Nextera L.monocytogenes'
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/pipeline_tests/Nextera_L.monocytogenes.info
contigs-ecoli-jgi-lane7:
name: 'Contigs 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/pipeline_tests/Contigs_E.coli_JGI_lane7.info
fullrun-mruber-jgi-lane9:
name: 'Full run 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/pipeline_tests/Full_run_M.ruber_JGI_lane9_prenormalized.info
iontorrnent-ecoli-k12:
name: 'IonTorrent E.coli K12'
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/pipeline_tests/IonTorrent_E.coli_K12.info
mate-pair-bfaecium:
name: 'Mate-pairs B.faecium'
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/pipeline_tests/Mate-pairs_B.faecium.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/pipeline_tests/Single-cell_P.heparinus_JGI_lane7_prenormalized.info
plasmid-ccallunae:
name: 'plasmidSPAdes C.callunae'
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/pipeline_tests/plasmidSPAdes_C.callunae.info
single-reads-ecoli-deeptrench:
name: 'Single reads 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/pipeline_tests/Single_reads_E.coli_deeptrench.info
pacbio-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@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/PacBio_M.ruber.info
saves-ecoli-100k:
name: 'Saves E.coli 100K'
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/pipeline_tests/Saves_E.coli_100K.info
saves-ecoli-ucsd-lane1:
name: 'Saves 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/pipeline_tests/Saves_E.coli_UCSD_lane1.info
metaspades-jgi-150:
name: 'metaSPAdes JGI 150'
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/pipeline_tests/metaSPAdes_JGI_150.info
metaviral-test:
name: 'metaviralSPAdes ERR525599'
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/pipeline_tests/metaviral_test.info