conda create -y -n nf-env -c conda-forge -c bioconda openjdk==11.0.20 singularity nextflow=22.10.0 git bowtie2 cxx-compiler glpk graphviz mamba
conda activate nf-env
mkdir resources mkdir resources/v1.4
wget https://apps-01.i-med.ac.at/resources/nextneopi/nextNEOpi_1.4_resources.tar.gz
tar -xvzf nextNEOpi_1.4_resources.tar.gz
Download request: https://w3.genome.med.kyoto-u.ac.jp/HLA-HD/
wget https://w3.genome.med.kyoto-u.ac.jp/HLA-HD/filedownload/hlahd.1.7.0.tar.gz
tar -zxvf hlahd.1.7.0.tar.gz
sh install.sh
Request license for mixcr https://licensing.milaboratories.com/
export TMP="/mnt/SCS/data_2/Users/Willem/tmp" export SINGULARITY_TMPDIR="/mnt/SCS/data_2/Users/Willem/tmp" export NXF_SINGULARITY_CACHEDIR="/mnt/SCS/data_2/Users/Willem/tmp" export PATH=$PATH:/mnt/SCS/data_2/Users/Willem/EMC-Neoantigen/bin/hlahd.1.7.0/bin
If you want to test the pipeline using a working minimal test dataset you may download one from https://apps-01.i-med.ac.at/resources/nextneopi/nextNEOpi_testdata.tar.gz
tar -zxvf nextNEOpi_testdata.tar.gz
// Directories (need to be in quotes) tmpDir = "/mnt/SCS/data_2/Users/Willem/tmp" // Please make sure that there is enough free space (~ 50G) // workDir = "/mnt/FS2/data_1/TESLA-Neoantigen/Tools/work" outputDir = "/mnt/SCS/data_1/TESLA-Neoantigen/Results"
sudo singularity build --sandbox pva_pvac_vt pva_pvac_vt.def sudo singularity build pva_pvac_vt.sif pva_pvac_vt cp pva_pvac_vt.sif apps-01.i-med.ac.at-images-singularity-pVACtools_4.0.1_icbi_4ae2625d.sif
nextflow run nextNEOpi.nf --batchFile TESLA_ID1.csv -profile singularity -config conf/params.config --accept_license -resume