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AstrobioMike / GToTree

A user-friendly workflow for phylogenomics
GNU General Public License v3.0
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Using gtt-data-locations set with singularity image #93

Closed nandan75 closed 5 months ago

nandan75 commented 5 months ago

Hi,

Thanks for making this wonderful tool.

I am using the singularity image of the gToTree tool from https://quay.io/repository/biocontainers/gtotree?tab=tags

When trying to set the gtt-data-locations using gtt-data-locations set

I get the followign error.

We can't seem to find a place to store startup environmental variables
  :( '
  This is likely due to permission restrictions in the conda environment
  location, and in your home location.

I wanted to use your tool to be part of my nextflow pipeline.

Appreciate any assistance,

regards,

Nandan

AstrobioMike commented 5 months ago

Hi there, Nandan,

Did you think I would forget you asked this before (https://github.com/AstrobioMike/GToTree/issues/86), and I'd feel more pressure because more people were requesting it? Haha :) (not a bad play if so!)

Sorry, I still haven't been able to put time into getting things to work via Singularity. I took at peek at it, but I wasn't able to set locations for the needed reference files where there are write permissions inside the container. I'm sure there are ways to deal with this, but i just don't know them and haven't been able to sort it out :/

nandan75 commented 5 months ago

Oops my bad- I completely forgot my own query :-) No way I was trying to pressurise you.

It is just that I tried a few other tools on the way such as Phylophlan3 etc and found a few singularity related issues there and then came back to check on your good tool . And completely lost track that I had pestered you before. My apologies.

regards,

Nandan

On Fri, May 3, 2024 at 12:17 PM Mike Lee @.***> wrote:

Hi there, Nandan,

Did you think I would forget you asked this before (#86 https://github.com/AstrobioMike/GToTree/issues/86), and I'd feel more pressure because more people were requesting it? Haha :) (not a bad play if so!)

Sorry, I still haven't been able to put time into getting things to work via Singularity. I took at peek at it, but I wasn't able to set locations for the needed reference files where there are write permissions inside the container. I'm sure there are ways to deal with this, but i just don't know them and haven't been able to sort it out :/

— Reply to this email directly, view it on GitHub https://github.com/AstrobioMike/GToTree/issues/93#issuecomment-2092027758, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC4A5CJ5OVIIGXR6LGLYVX3ZALXUXAVCNFSM6AAAAABHEOBG4CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJSGAZDONZVHA . You are receiving this because you authored the thread.Message ID: @.***>

AstrobioMike commented 5 months ago

Haha, all good! I feel for you still trying to find a path that works for you :/ Wish I had better news from my end!