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Gabaldonlab / perSVade

perSVade: personalized Structural Variation detection
GNU General Public License v3.0
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mamba required for installation of dependencies #2

Closed SAMtoBAM closed 2 years ago

SAMtoBAM commented 2 years ago

Hi there,

I am installing perSVade through the generic system using conda (mamba not installed), however during the dependency installation step I get this error: ./installation/setup_environment.sh: line 74: mamba: command not found Meaning that it seems mamba has been made a requirement? can conda be used in the absence of mamba during the installation of these dependencies?

thanks

MikiSchikora commented 2 years ago

Good evening,

Right now mamba is required, yes. mamba works just like conda, but way faster. I could write a version of ./installation/setup_environment.sh that works with conda instead of mamba, but it would take very long to create all the environments and I don't think that it'd be practical.

The wiki shows how mamba should be installed in the base conda environment as a first step. I will clarify that this is necessary.

Would this be a good solution for futher users? Is there any reason by which you would not like to use mamba?

Hope this helps,

Miquel Àngel Schikora Barcelona Supercomputing Center

MikiSchikora commented 2 years ago

Hi again,

I think that this is already cleared. If you fave further questions, just re-open this comment.

Thanks,

Miquel Àngel Schikora Barcelona Supercomputing Center