Merge pull request #13 from griffithlab/evelyn-schmidt-patch-1

Update README.md

Author: evelyn-schmidt

README.md

@@ -75,12 +75,14 @@ exit
 To generate files needed for manual review, save the pVAC results from the Immunogenomics Tumor Board Review meeting as $SAMPLE.revd.Annotated.Neoantigen_Candidates.xlsx (Note: if the file is not saved under this exact name the below command will need to be modified).
 
 ```
-cd $WORKING_BASE/../manual_review
-bsub -Is -q oncology-interactive -G $GROUP -a "docker(griffithlab/neoang_scripts)" /bin/bash
+docker pull griffithlab/neoang_scripts
+docker run -it --env WORKING_BASE -v $HOME/:$HOME/ -v $HOME/.config/gcloud:/root/.config/gcloud griffithlab/neoang_scripts /bin/bash
 
-export SAMPLE="TWJF-10146-0029"
+cd $WORKING_BASE
 
-python3 /opt/scripts/setup_review.py -WB $WORKING_BASE -a ../itb-review-files/*.xlsx -c $WORKING_BASE/../generate_protein_fasta/candidates/annotated_filtered.vcf-pass-51mer.fa.manufacturability.tsv -samp $SAMPLE  -classI $WORKING_BASE/final_results/pVACseq/mhc_i/*.all_epitopes.aggregated.tsv -classII $WORKING_BASE/final_results/pVACseq/mhc_ii/*.all_epitopes.aggregated.tsv 
+python3 /opt/scripts/generate_reviews_files.py -a itb-review-files/*.xlsx -c generate_protein_fasta/candidates/annotated_filtered.vcf-pass-51mer.fa.manufacturability.tsv -classI gcp_immuno/final_results/pVACseq/mhc_i/*.all_epitopes.aggregated.tsv -classII gcp_immuno/final_results/pVACseq/mhc_ii/*.all_epitopes.aggregated.tsv -samp $GCS_CASE_NAME -o manual_review/
+
+python3 /opt/scripts/color_peptides51mer.py -p manual_review/*Peptides_51-mer.xlsx -samp $GCS_CASE_NAME -o manual_review/
 ```
 
 ## Creating Case Final Report locally