error in docker run step for uch file or directory

[xiangyupan]

Hi David,

Thanks for the probe design tools for RNA-FISH. People in my lab do bench work are all interested in the tools. I am major in bioinformatics in my lab, then they ask me to help run the probegenerator.
I am testing this in one fasta sequence, but a cascade error occurred. As I'm not familiar to docker, the error had borthered me for some time.
The error is in as follows:

The command is docker run --env-file=/gfsdata01/Users/PXY/Tail/probegenerator/MountFolder/env_file -v /gfsdata01/Users/PXY/Tail/probegenerator/MountFolder:/data dstein96/probegenerator:0.89
The files in MountFolder is as follows:

And the env_file is as follows:
seq_path=./SOX10.fa path_to_bowtie_index=/gfsdata01/Users/PXY/Tail/probegenerator/Axolotl_v6_index bowtie_index_basename=Axolotl_v6_index initiator=/gfsdata01/Users/PXY/Tail/probegenerator/MountFolder desired_spaces=3 l=25 L=25 g=40 G=60 t=37 T=72 s=1000 F=30
And the gene fasta is as follows:

Hope for your help. Thanks for your time and work.
Best,
Xiangyu

[davidfstein]

Hi Xiangyu,

Apologies for the slow response, I haven't been monitoring this repository. I think if you update the paths in your envfile to be relative to the mount folder, it should work for you. So "/gfsdata01/Users/PXY/Tail/probegenerator/Axolotl_v6_index" would become "Axolotl_v6_index" etc. What is happening is the MountFolder is being mounted at the path /data in the docker container. So all the stuff in your mount folder is available inside the "/data" folder and that is where the program will be looking for it.

Best,
David