BigMHC prediction not working

giacuong171 commented 4 months ago

Installation Type

Standalone

pVACtools Version / Docker Image

4.2.1

Python Version

3.10.8

Operating System

Linux

Describe the bug

The error occurs when pvactools run BigMHC prediction. It seems that there is no tool named bigmhc_predict, that is installed with pvactools. Should I install it separately from this repo ?

How to reproduce this bug

pvacseq run \
input.vcf.gz \
sample_name \
HLA-A*01:01,HLA-A*68:02,HLA-B*08:01,HLA-B*37:01,HLA-C*06:03,HLA-C*07:01 \
all \
output \
--normal-sample-name normal_sample_name \
-e1 8,9,10 \
-e2 15 \

Input files

No response

Log output

The full log file is : pvactools.log

Output files

No response

susannasiebert commented 4 months ago

BigMHC, as well as DeepImmuno, need to be installed separately. Please follow the instructions in our documentation to install these predictors. Please note, that these instructions are different from the installation instructions provided by BigMHC and DeepImmuno directly. pVACtools will only be able to use BigMHC and DeepImmuno if it is installed as instructed in our documentation.

giacuong171 commented 4 months ago

Thank you for your quick response. I installed pvactools using pip and wonder if the Docker image of pvactools already includes BigMHC or DeepImmuno, or if I need to install them separately ?

susannasiebert commented 4 months ago

Our Docker image comes with both BigMHC and DeepImmuno pre-installed.

griffithlab / pVACtools