error in the dockerfile

[weizhu365]

In the docker file, all scripts were copied to /rocker-build

ls -al /rocker-build/
total 83
drwxr-xr-x 3 root   root     323 May  3 16:10 .
drwxr-xr-x 1 zhuw10 zhuw10   100 Aug 14 16:18 ..
-rwxrwxr-x 1 root   root    2106 Apr 29 13:07 01-filter_vcf.sh
-rw-rw-r-- 1 root   root   22709 Apr 29 13:07 02-annotate_variants_CAVATICA_input.R
-rw-rw-r-- 1 root   root   21769 Apr 29 13:07 02-annotate_variants_custom_input.R
-rw-rw-r-- 1 root   root    1566 Apr 29 13:07 03-parse_vcf.sh
-rw-rw-r-- 1 root   root    8419 May  3 16:04 04-filter_gene_annotations.R
drwxrwxr-x 8 root   root    2750 May  3 16:10 bcftools-1.17
-rw-rw-r-- 1 root   root    1411 May  3 16:08 Dockerfile
-rw-rw-r-- 1 root   root     911 Apr 29 13:07 download_db_files.sh
-rw-rw-r-- 1 root   root    9230 Apr 29 13:07 run_autogvp.sh
-rw-rw-r-- 1 root   root   13778 Apr 29 13:07 select-clinVar-submissions.R

The launch of the script run_autogvp.sh needs the script like "download_db_files.sh" under the folder /rocker-build/scripts (not /rocker-build). I recommend to use git clone to install the repo to the container, rather than to use COPY.

Thanks,

Wei Zhu