https://github.com/likelet/lohhlaenvfastbuild
Build LOHHLA run env with a simple script
https://github.com/likelet/lohhlaenvfastbuild
Last synced: 18 days ago
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Build LOHHLA run env with a simple script
- Host: GitHub
- URL: https://github.com/likelet/lohhlaenvfastbuild
- Owner: likelet
- Created: 2022-05-20T04:43:22.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2022-05-31T06:25:54.000Z (about 4 years ago)
- Last Synced: 2025-11-17T19:03:20.820Z (8 months ago)
- Language: Shell
- Size: 20.5 KB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# LOHHLA run environemnt
Install [LOHHLA](https://github.com/mskcc/lohhla) run environment is painful as little information provided by the authors. Here I present a fast installation script to build enssential depdendencies to run at least test dataset
## Quick configure
```shell
# clone this repo
git clone https://github.com/likelet/LOHHLAenvFastbuild.git & cd LOHHLAenvFastbuild
# run install env
bash Buildenv.sh
```
## Note to run exmaples
1. Please make sure that the `--gatkDir`, `--novoDir`,`--HLAexonLoc` were configured.
## Run the following test code
```shell
# set home dir
# mk out folder
mkdir test_out
locationDIR="${HOME}/lohhla" # the home of the lohhla software
ourDir="./test_out"
Rscript ${locationDIR}/LOHHLAscript.R --patientId example --outputDir $outDir \
--normalBAMfile ${locationDIR}/example-file/bam/example_BS_GL_sorted.bam --BAMDir ${locationDIR}/example-file/bam/ \
--hlaPath ${locationDIR}/example-file/hlas \
--HLAfastaLoc ${locationDIR}/data/example.patient.hlaFasta.fa \
--CopyNumLoc ${locationDIR}/example-file/solutions.txt \
--mappingStep TRUE --minCoverageFilter 10 --fishingStep TRUE --cleanUp FALSE \
--gatkDir ${HOME}/bin/picard \
--novoDir ${HOME}/miniconda3/envs/lohhla/bin/novoalign \
--HLAexonLoc ${locationDIR}/data/hla.dat
```
This code also be found at the run-example.sh in lohhla folder.
## Credit.
This script was inspired by Yanxing Chen as well as Shixiang Wang from SYSUCC
If you use LOHHLA in your research, please cite the following paper:
>McGranahan et al., Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution, Cell (2017), https://doi.org/10.1016/j.cell.2017.10.001