update image to include STAR aligner #38
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # This is a basic workflow to Test HiCUP | |
| name: HiCUP+ Test (Bowtie2) | |
| # Controls when the action will run. Triggers the workflow on push or pull request | |
| # events but only for the master branch | |
| on: | |
| push: | |
| branches: [ master, devel, actions ] | |
| pull_request: | |
| branches: [ master, devel, actions ] | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| # This workflow contains a single job called "build" | |
| build: | |
| # The type of runner that the job will run on | |
| runs-on: ubuntu-latest | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - uses: actions/checkout@v2 | |
| # Runs a single command using the runners shell | |
| - name: Run a one-line script | |
| run: echo Hello, world! | |
| # Runs a set of commands using the runners shell | |
| - name: Update Ubuntu | |
| run: | | |
| sudo apt-get update | |
| - name: Install dependencies | |
| run: | | |
| sudo apt install samtools | |
| sudo apt install bowtie2 | |
| sudo apt install r-base-core | |
| - name: Download Test Dataset and genome index files and FASTA files | |
| run: | | |
| wget -nv https://www.bioinformatics.babraham.ac.uk/projects/hicup/test_dataset.tar.gz | |
| tar xvzf test_dataset.tar.gz | |
| mkdir -p Homo_sapiens.GRCh38_Bowtie2_Index_HiCUP | |
| cd Homo_sapiens.GRCh38_Bowtie2_Index_HiCUP | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes/Human/Homo_sapiens.GRCh38.1.bt2 | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes/Human/Homo_sapiens.GRCh38.2.bt2 | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes/Human/Homo_sapiens.GRCh38.3.bt2 | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes/Human/Homo_sapiens.GRCh38.4.bt2 | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes/Human/Homo_sapiens.GRCh38.rev.1.bt2 | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes/Human/Homo_sapiens.GRCh38.rev.2.bt2 | |
| cd .. | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.2.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.3.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.4.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.5.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.6.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.7.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.8.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.9.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.10.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.11.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.12.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.13.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.14.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.15.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.16.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.17.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.18.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.20.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.22.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.MT.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.X.fa.gz | |
| wget -nv http://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes_Bisulfite/Human/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.Y.fa.gz | |
| - name: Run HiCUP | |
| run: | | |
| $GITHUB_WORKSPACE/hicup --help | |
| $GITHUB_WORKSPACE/hicup --version | |
| $GITHUB_WORKSPACE/hicup_digester --re1 A^AGCTT,HindIII --genome Human38 --zip *.fa.gz | |
| $GITHUB_WORKSPACE/hicup --digest Digest* --zip --threads 2 --index ./Homo_sapiens.GRCh38_Bowtie2_Index_HiCUP/Homo_sapiens.GRCh38 --shortest 50 --longest 700 test_dataset/*.fastq | |
| - name: Check results | |
| run: | | |
| $GITHUB_WORKSPACE/Testing/hicup_checker --threshold 5 --expected test_dataset/HiCUP_summary_test_dataset_results.txt --new HiCUP_summary_report_* |