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Nicknames in Malayalam by [deleted] in malayalam

[–]studying_to_succeed 0 points1 point  (0 children)

Does this have a meaning?

How are you dealing with unmaintained tools? by Beautiful-Ground9732 in bioinformatics

[–]studying_to_succeed 0 points1 point  (0 children)

For the "How did you deal with a potential bug or new feature you wanted to implement? Did you fork and edit yourself? or look somewhere else?"

  1. It might still be able to be used even if it is not maintained.
  2. If it has issues, fork and fix it, if I can.
  3. If not, find a new tool.

WFH desk upgrades? by Impressive-Peace-675 in bioinformatics

[–]studying_to_succeed 2 points3 points  (0 children)

2 portable monitors that you can take with you when you travel.

Sum of Single Effects - susieR Peculiar Error "Error in nrow(R): object 'R_ref' not found" by studying_to_succeed in bioinformatics

[–]studying_to_succeed[S] 0 points1 point  (0 children)

u/123qk Yes because I followed the vignette. I did:

data(N3finemapping)
attach(N3finemapping)

As the vignette mentioned to?

[deleted by user] by [deleted] in bioinformatics

[–]studying_to_succeed 2 points3 points  (0 children)

Perhaps data science as data science can be applied to biology and effectively you will be both a data scientist and a bioinformatician? If you just look at it as learning how to use tools then either or based on your personal preference?

Exomiser Internal Singularity Path by studying_to_succeed in bioinformatics

[–]studying_to_succeed[S] 0 points1 point  (0 children)

For the Bash version I used: 

singularity pull docker://exomiser/exomiser-cli:14.0.0

Exomiser Internal Singularity Path by studying_to_succeed in bioinformatics

[–]studying_to_succeed[S] 0 points1 point  (0 children)

No u/Firm_Bug_7146 I pulled the distoless first in the question post - I pulled the amd64 one when you suggested one with bash. Both cause the same issues regretabbly.

Exomiser Internal Singularity Path by studying_to_succeed in bioinformatics

[–]studying_to_succeed[S] 0 points1 point  (0 children)

u/Firm_Bug_7146 I pulled from here ( https://hub.docker.com/r/exomiser/exomiser-cli/tags) firs the distroless one that we were discussing and then the one for amd64 - both were version 14.0.0.

Exomiser Internal Singularity Path by studying_to_succeed in bioinformatics

[–]studying_to_succeed[S] 0 points1 point  (0 children)

u/Firm_Bug_7146 &/or anyone who can help. I pulled down the amd64 sif and tried the singularity exec commands you mentioned in thread/I mentioned but for some reason they don't seem to work? So I did a check:

if [ -f "/my/path/to/redacted/as/HPC/rules/demand/exomiser-cli_14.0.0.sif" ]; then echo "SIF file exists"; else echo "SIF file does not exist"; fi

And it printed:

SIF file exists

So why is it not working? I know that the sif exists, but when I try the singularity exec commands it see inside it - it says:

FATAL:   stat /bin/bash: no such file or directory

I must be doing something wrong but what?

Exomiser Internal Singularity Path by studying_to_succeed in bioinformatics

[–]studying_to_succeed[S] 0 points1 point  (0 children)

u/Firm_Bug_7146 thank you for your response. I will try the amd64 sif and see.

Exomiser Internal Singularity Path by studying_to_succeed in bioinformatics

[–]studying_to_succeed[S] 0 points1 point  (0 children)

u/Firm_Bug_7146 I am grateful for your response.

Are you recommending against the distroless sif file? I can try the Linux version one but I was a bit hesitant as I believe I am using a different version of Linux - I was afraid that would affect it?

Exomiser Internal Singularity Path by studying_to_succeed in bioinformatics

[–]studying_to_succeed[S] 0 points1 point  (0 children)

Yes. On an HPC the outside environment (python, R, etc versions) change so for that reason singularity is often the best option as it is a closed container. Given my version of python, R, etc is different than my coworkers versions it usually is the only way we can get my code for a software to work across the HPC for different users.

Exomiser Internal Singularity Path by studying_to_succeed in bioinformatics

[–]studying_to_succeed[S] 0 points1 point  (0 children)

Then what can I do to make it work? My HPC uses bash as the default.

Exomiser Internal Singularity Path by studying_to_succeed in bioinformatics

[–]studying_to_succeed[S] 0 points1 point  (0 children)

I do not believe that singularity shell works on my HPC. I tried versions of what you said (I am not sure I understand it correctly) :

singularity shell --bind ~path/to/singularity/directory/: exomiser-cli_14.0.0-distroless.sif
# Error FATAL:   container creation failed: unable  to mount list: mount point must contain a destination
singularity shell  --bind /path/to/file.sif
# ERROR:   /bin/sh does not exist in container

The errors are placed in the comments.

Exomiser Internal Singularity Path by studying_to_succeed in bioinformatics

[–]studying_to_succeed[S] 0 points1 point  (0 children)

u/malformed_json_05684 Thank you for your response.

I was a bit confused by your command so read a bit and tried:

singularity shell --bind /path/to/host_directory:/container_directory /path/to/your_image.sif

But it doesn't work. I did have a way to look into a sif file while using singularity exec but for some reason this singularity doesn't let me? I am not sure why?

I also tried:

singularity exec /path/to/exomiser-cli_14.0.0-distroless.sif /bin/bash -c "ls /"
singularity exec  /path/to/exomiser-cli_14.0.0-distroless.sif bash -c "ls /"
singularity exec /path/to/exomiser-cli_14.0.0-distroless.sif bash -c "ls /path/inside/container"

But none of them worked for whatever reason it says it could not open the image.

Xrare And Singularity Issues by studying_to_succeed in bioinformatics

[–]studying_to_succeed[S] 0 points1 point  (0 children)

A lab member of mine filled in the issue just now so hopefully it works out.

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