Week 9 quiz - #8

Courses ABCD ReproNim
1

Hello all,

I have read the previous help for question 8, but unfortunately, it does not fix the problem. I am currently running datalad containers on Centos 7. When I put in the following commands: datalad containers-run -n fsl --explicit --input data/sub-01/anat/sub-01_T1w.nii.gz --output derivatives/first/sub-01 run_first_all -i data/sub-01/anat/sub-01_T1w.nii.gz -o derivatives/first/sub-01/none -m none -s L_Hipp,R_Hipp
I get the following:
[INFO ] Making sure inputs are available (this may take some time)
[INFO ] == Command start (output follows) =====
/bin/sh: singularity: command not found
[INFO ] == Command exit (modification check follows) =====
[INFO ] The command had a non-zero exit code. If this is expected, you can save the changes with ‘datalad save -d . -r -F .git/COMMIT_EDITMSG’
CommandError: ‘singularity exec --cleanenv .datalad/environments/fsl/image run_first_all -i data/sub-01/anat/sub-01_T1w.nii.gz -o derivatives/first/sub-01/none -m none -s L_Hipp,R_Hipp’ failed with exitcode 127 under /home/mcalvert/week9_analysis

Thank you!

Maegan

2

Hi @maeganlcalvert,

This error /bin/sh: singularity: command not found suggests to me that singularity is not installed/available on the machine you are working on.
To confirm, you can try typing singularity --version in your terminal and see if you get the same error: singularity: command not found.

If the machine also has a bash environment (as opposed to sh), perhaps there are updated paths that make singularity accessible, so you could try 1) type bash, then 2) type singularity --version, to see if singularity is installed.

Hope that helps!
James

3

Thank you! That was the problem!