script to run inside docker hub image samesense/ngs_plot

docker_ngs.plot_usage.sh

# Use this inside https://hub.docker.com/r/samesense/ngs_plot/

# set env variables
alias python='/condas/miniconda3/bin/python'
export PATH=/condas/miniconda3/bin/:$PATH
export NGSPLOT=/bin/ngsplot
export PATH=/bin/ngsplot/bin/:$PATH
source /condas/miniconda3/bin/activate py27

# cannot write in default dir
# so change to write able dir
cd /mnt/isilon/cbmi/variome/perry/tmp/

ngs.plot.r -G hg19 -R bed \
-E /mnt/isilon/gerdblobel_lab/perry/mike_sarcoma_chipseq/data/interim/macs2_peaks/sraFli1_summits.sort.bed \
-C /mnt/isilon/gerdblobel_lab/perry/mike_sarcoma_chipseq/work/ngsplot/all.fli1Peaks.config -O all_sraFliPeaks -T Tot -L 2000 -GO none

# mv results
mv all_sraFliPeaks.*pdf /mnt/isilon/gerdblobel_lab/perry/mike_sarcoma_chipseq/docs/plot/

Hi, do you have any suggestions on how to run the dockerimage for ngsplot and then use this script of yours?

Something like this using zsh on macOS

docker run -it -v $(pwd):/data samesense/ngs_plot bash

thanks!