Can't running bash script with singularity

[WKabza]

Version of Singularity:

3.5.3

Expected behavior

I am trying to run a bash script using a container within singularity singularity run Delly.simg Delly_script.sh

Actual behavior

/.singularity.d/runscript: exec: line 39: Delly_script.sh: not found

How did you install Singularity

It was already on the server :/

[jmstover]

What does your %runscript section look like? Do you get the same error with singularity exec ?

[WKabza]

What does your %runscript section look like? Do you get the same error with singularity exec ?

I am having the same error with singularity exec /.singularity.d/actions/exec: exec: line 21: Delly_script.sh: not found

I have not defined a runscript and I was importing a Docker container.

The script is in the same place as my container.

# Recipe

Bootstrap: docker
From: dellytools/delly

%runscript
singularity exec Delly.simg/ Delly_script.sh

[jmstover]

. isn't in the PATH ... try putting ./Delly_script.sh (or full path) instead of just the name of the script.

I just built that image with the following definition file:

$ cat delly.def 
# Recipe

Bootstrap: docker
From: dellytools/delly

And ran the following:

$ /usr/local/singularity/3.5.3/bin/singularity exec delly.sif ./delly_script.sh 
Hello world from ./delly_script.sh running in delly.sif

The delly_script.sh file looks like:

#!/bin/sh

echo "Hello world from $0 running in ${SINGULARITY_NAME}"

The delly_script.sh is in my working directory and gets bind mounted in (current working directory mount). Where is your Delly_script.sh file at? run also works because of how the default runscript is created on this container:

$ /usr/local/singularity/3.5.3/bin/singularity run delly.sif ./delly_script.sh 
Hello world from ./delly_script.sh running in delly.sif

[WKabza]

. isn't in the PATH ... try putting ./Delly_script.sh (or full path) instead of just the name of the script.

I just built that image with the following definition file:

$ cat delly.def 
# Recipe

Bootstrap: docker
From: dellytools/delly

And ran the following:

$ /usr/local/singularity/3.5.3/bin/singularity exec delly.sif ./delly_script.sh 
Hello world from ./delly_script.sh running in delly.sif

The delly_script.sh file looks like:

#!/bin/sh

echo "Hello world from $0 running in ${SINGULARITY_NAME}"

The delly_script.sh is in my working directory and gets bind mounted in (current working directory mount). Where is your Delly_script.sh file at? run also works because of how the default runscript is created on this container:

$ /usr/local/singularity/3.5.3/bin/singularity run delly.sif ./delly_script.sh 
Hello world from ./delly_script.sh running in delly.sif

I forgot to mention that I am trying to run this script with bash, not dash #!/bin/bash I am having this problem when running with bash: /.singularity.d/actions/exec: exec: line 21: Delly_script.sh: not found

and this problem when running with dash sh Delly_script.sh: line 13: syntax error: unexpected "(" Of course I get the case that other interpreter (in this case dash) does not support arrays as Bash does.

Can you try run your script with #!/bin/bash interpreter, please?

Also

. isn't in the PATH ... try putting ./Delly_script.sh (or full path) instead of just the name of the script.

this didn't work :(

[jmstover]

Bash isn't in the container image... The delly base image is alpine which has a busybox root. /bin/sh in the image points to busybox which IIRC is an ash shell.

Singularity> delly -v
delly -v
Delly version: v0.8.3
 using Boost: v1.65.1
 using HTSlib: v1.10.2

Singularity> ls -l /bin/sh
ls -l /bin/sh
lrwxrwxrwx    1 root     root            12 May 29 09:20 /bin/sh -> /bin/busybox

I think in a %post section you need to do something like:

apk update
apk add bash

But I haven't used Alpine / apk much, so that's a guess....

[WKabza]

Thank you for this information! That was very helpful to understand.

Also I have checked what interpreters are on my server

cat /etc/shells
/bin/sh
/bin/bash
/sbin/nologin
/usr/bin/sh
/usr/bin/bash
/usr/sbin/nologin
/bin/ksh
/bin/rksh
/bin/tcsh
/bin/csh
/bin/zsh

bash --version
GNU bash, version 4.2.46(2)-release (x86_64-redhat-linux-gnu)
Copyright (C) 2011 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>

and tried: singularity run --writable Delly.simg/ apk add --no-cache bash

but I have this error:

fetch http://dl-cdn.alpinelinux.org/alpine/v3.12/main/x86_64/APKINDEX.tar.gz
fetch http://dl-cdn.alpinelinux.org/alpine/v3.12/community/x86_64/APKINDEX.tar.gz
10 errors; 8 MiB in 18 packages

Maybe that deserves a new issue to make on forum.

[jmstover]

singularity run --writable Delly.simg/ apk add --no-cache bash

Use sudo .... I'm assuming the image was created as root, so you would have root owned files. I'm not sure if apk can be ran as a non-root user, or if it may fail.

[WKabza]

singularity run --writable Delly.simg/ apk add --no-cache bash

Use sudo .... I'm assuming the image was created as root, so you would have root owned files. I'm not sure if apk can be ran as a non-root user, or if it may fail.

I have not use sudo command because from the beginning I am having problem with it sudo: singularity: command not found

[jmstover]

In the /etc/sudoers file, the secure_path value is probably set and doesn't have the path to the singularity binary in it.

[WKabza]

Eventually my problem was not solved because I got information that users of my server are not allowed to use sudo command and probably this is the cause I can't add bash to my container. Nonetheless all those information here were very helpful for me, thank you!!

[hqzhou]

Recipe

Bootstrap: docker From: dellytools/delly

%runscript singularity exec Delly.simg/ Delly_script.sh

change the content of %runscript into: exec /path/to/Delly_script.sh