update ReadTheDocs (test) #46
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| # 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 | |
| sudo apt install bioperl | |
| - name: Test all perl scripts | |
| run: | | |
| $GITHUB_WORKSPACE/hicup --help | |
| $GITHUB_WORKSPACE/hicup --version | |
| $GITHUB_WORKSPACE/hicup_mapper --help | |
| $GITHUB_WORKSPACE/hicup_digester --help | |
| $GITHUB_WORKSPACE/hicup_truncater --help | |
| $GITHUB_WORKSPACE/hicup_deduplicator 2>&1 | grep Please | |
| $GITHUB_WORKSPACE/Conversion/hicup2hicpipe --help | |
| $GITHUB_WORKSPACE/Conversion/hicup2gothic --help | |
| $GITHUB_WORKSPACE/Conversion/hicup2fithic --help | |
| $GITHUB_WORKSPACE/Conversion/hicup2homer --help | |
| $GITHUB_WORKSPACE/Conversion/hicup2juicer --help | |
| $GITHUB_WORKSPACE/Conversion/hicup2ncc --help | |
| $GITHUB_WORKSPACE/Misc/find_common_fragment_interactions.pl --help || [[ $? == 255 ]] | |
| $GITHUB_WORKSPACE/Misc/hicup_capture --help | |
| $GITHUB_WORKSPACE/Misc/make_hic_array.pl || [[ $? == 255 ]] | |
| $GITHUB_WORKSPACE/scribler/scribler --help | |
| $GITHUB_WORKSPACE/scribler/scribl_capture_ditag_sorter.pl || [[ $? == 255 ]] | |
| $GITHUB_WORKSPACE/scribler/scribl_capture.pl || [[ $? == 255 ]] | |
| $GITHUB_WORKSPACE/scribler/scribl_capture_region_breakdown.pl || [[ $? == 255 ]] | |
| - name: Download Test Dataset 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 | |
| wget -nv https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr21.fa.gz | |
| wget -nv https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr22.fa.gz | |
| cat chr*.fa.gz | gunzip > chr21chr22_hg38.fa | |
| - name: Build bowtie2 index | |
| run: | | |
| mkdir -p chr21chr22_hg38 | |
| bowtie2-build chr21chr22_hg38.fa chr21chr22_hg38/chr21chr22_hg38 | |
| - name: Run HiCUP | |
| run: | | |
| $GITHUB_WORKSPACE/hicup_digester --re1 A^AGCTT,HindIII --genome Human38chr21and22 --zip chr21chr22_hg38.fa | |
| $GITHUB_WORKSPACE/hicup --bowtie2 $(which bowtie2) --digest Digest* --zip --threads 2 --index ./chr21chr22_hg38/chr21chr22_hg38 --shortest 50 --longest 700 test_dataset/*.fastq | |
| - name: Check results | |
| run: | | |
| $GITHUB_WORKSPACE/Testing/hicup_checker --threshold 5 --expected $GITHUB_WORKSPACE/Testing/test_output/HiCUP_summary_report_lHWLvpbSoZ_13-54-49_16-02-2023.txt --new HiCUP_summary_report_* |