Singularity use

[lgmgeo]

Hi,

First of all, thanks for PennCNV, it's a great tool!

I would like to use singularity (I'm really not an expert) but my attempts remained unsuccessful

Here are the commands I run:

singularity pull penncnv.sif docker://genomicslab/penncnv
singularity exec penncnv.sif detect_cnv.pl -h

But I got the following error message:

/.singularity.d/actions/exec: line 21: exec: detect_cnv.pl: not found

Thank you for any help you can provide me,

Véronique

[kaichop]

can you supply the full path /home/user/PennCNV/detect_cnv.pl in the command.

On Fri, Jan 6, 2023 at 6:50 AM Geoffroy Véronique @.***> wrote:

Hi,

First of all, thanks for PennCNV, it's a great tool!

I would like to use singularity (I'm really not an expert) but my attempts remained unsuccessful

Here are the commands I run:

singularity pull penncnv.sif docker://genomicslab/penncnv

singularity exec penncnv.sif detect_cnv.pl -h

But I got the following error message:

/.singularity.d/actions/exec: line 21: exec: detect_cnv.pl: not found

Thank you for any help you can provide me,

Véronique

— Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/98, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OHLA3NM7TKUS6DWZ63WRABHZANCNFSM6AAAAAATS763JA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[lgmgeo]

Thank you for your help ;o)

To resume all the install steps:

cd /home/user/
git clone https://github.com/WGLab/PennCNV.git
singularity pull penncnv.sif docker://genomicslab/penncnv

To run:

singularity exec penncnv.sif /home/user/PennCNV/detect_cnv.pl -h

Is it correct?

[kaichop]

Try it, I do not know and have no experience, but supplying full path solves the 'exec not found' problem. You can also invoke an interactive shell and then run penncnv commands within the shell.

On Fri, Jan 6, 2023 at 12:09 PM Geoffroy Véronique @.***> wrote:

Thank you for your help ;o)

To resume all the install steps:

cd /home/user/ git clone https://github.com/WGLab/PennCNV.git singularity pull penncnv.sif docker://genomicslab/penncnv

To run:

singularity exec penncnv.sif /home/user/PennCNV/detect_cnv.pl -h

Is it correct?

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[lgmgeo]

Thank you very much, the help command is working. I will run PennCNV on our data.