running docker image in singularity

14 views
Skip to first unread message

Cen T

unread,
Jan 5, 2022, 1:04:39 PM1/5/22
to apollo
Anyone can help me run docker image in singularity?

I ran singularity using this command:

singularity run --bind .:/data docker://gmod/apollo:stable
INFO:    Using cached SIF image
Password:


Since I'm prompted for a password. I tried inputting "password" but it came back "Authentication failure". Putting "password" twice will get me to this far:

chmod: changing permissions of '/var/run/postgresql': Read-only file system
WEBAPOLLO_HOST_FLAG:
CHADO_HOST_FLAG:
Waiting for DB
./var/run/postgresql:5432 - no response

Can someone advise on what to do?

Thank you in advance for your help.
Cen

Garrett Stevens

unread,
Jan 5, 2022, 8:23:00 PM1/5/22
to Cen T, apollo
I don't use Singularity, but the "Password" isn't anything from the Apollo Docker image, so it must be something to do with Singularity. Maybe it has to do with credentials for pulling the Docker image?

It looks like your Docker container does start, but I couldn't say why it fails on Postgres setup. The first few lines of output when I start a container are:

 * Starting PostgreSQL 9.6 database server                                                                                                                                     [ OK ]
WEBAPOLLO_HOST_FLAG:
CHADO_HOST_FLAG:
Waiting for DB
/var/run/postgresql:5432 - accepting connections
Postgres is up, configuring database

I would try running it in Docker without singularity first and refer to this guide. Also, make sure your current directory "." is a valid JBrowse data directory.

Best,
Garrett

--
To unsubscribe from this group and stop receiving emails from it, send an email to apollo+un...@lbl.gov.

Cen T

unread,
Jan 6, 2022, 11:10:22 AM1/6/22
to apollo, stevens....@gmail.com, apollo, Cen T
Thank you for your reply. 
I don't currently have access to Docker. I'll try to get one. 
Thanks for the hint. My current directory is not a JBrowse data directory. Do I need to install JBrowse?
Your postgres was showing accepting connections. Is 5432 the port number it is accepting connection? I wonder if that port is not available on my end. 

Thanks,
Cen

Reply all
Reply to author
Forward
0 new messages