Realize virtual environment on server

federicacitarrella / FusionFlow

FusionFlow is a bioinformatic pipeline that enables the detection of gene fusions from RNA and DNA data.

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Realize virtual environment on server #2

Closed Bontempogianpaolo1 closed 3 years ago

Bontempogianpaolo1 commented 3 years ago

This environment should be a temporary and safe workspace on a server in order to figure out how everything works

federicacitarrella commented 3 years ago

Can I use Conda to create this environment or do you suggest something else?

Bontempogianpaolo1 commented 3 years ago

As I know conda is already a good tool able to encapsulate python packages... you can use whatever you want! Just keep in mind this:

We are going to use docker in the future so keep trace of any change you do
Python is good and easy to write but also known to be slow respect to other languages. So there will be processes in your pipelines written in other languages like java or c++

federicacitarrella commented 3 years ago

Virtual environment creation on Philae using Conda:

Conda installation: wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh chmod -x Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-x86_64.sh

Virtual environment creation: conda create --name pipelineEnv

environment location: /home/citarrella/miniconda3/envs/pipelineEnv

federicacitarrella commented 3 years ago

I also looked for Java and C++ package manager and I saved the relative links in "Package manager: useful links" #8 issue in case of need.