Commit b22654a8 authored by Tru  HUYNH's avatar Tru HUYNH

anaconda2/3

parent eabac9c9
Anaconda2: provides python2 with its own conda package management system,
that can be user installed. If you happen you have non python3 friendly code.
+ easy way to take care of python2
+ one shot installation
+ one can use pip to add non anaconda packaged python modules (caveat don't overwrite
conda managed packages!)
- as any package management system, you depend on a 3rd party
- some conda packages might have non compatible requirements
Used by MICCA, picrust (Claudio)
see list of installed anaconda2 packages at:
(conda list output)
https://gitlab.pasteur.fr/tru/BGA2017/raw/master/noc-auth/BGA2017/installation_notes/anaconda2-list
1) Download and install
```
cd /BGA2017/sources/claudio
wget https://repo.continuum.io/archive/Anaconda2-4.3.1-Linux-x86_64.sh
sh /BGA2017/sources/claudio/Anaconda2-4.3.1-Linux-x86_64.sh -b -p /BGA2017/anaconda2
```
2) create the modulefile
```
wget -O /BGA2017/modulefiles/anaconda2 https://gitlab.pasteur.fr/tru/BGA2017/raw/master/noc-auth/BGA2017/modulefiles/anaconda2
```
3) update and add more packages
```
module use /BGA2017/modulefiles
module add anaconda2
conda update -y conda
conda update -y --all
conda install biopython
conda install cutadapt
conda install biom-format
```
Anaconda3: provides python3 with its own conda package management system,
that can be user installed.
+ easy way to take care of python3
+ one shot installation
+ one can use pip to add non anaconda packaged python modules (caveat don't overwrite
conda managed packages!)
- as any package management system, you depend on a 3rd party
- some conda packages might have non compatible requirements
Provides Jupyter Notebook (Gary)
see list of installed anaconda2 packages at:
(conda list output)
https://gitlab.pasteur.fr/tru/BGA2017/raw/master/noc-auth/BGA2017/installation_notes/anaconda3-list
1) Download and install
```
# Jupyter Notebook and Python/anaconda
cd /BGA2017/sources/gbenson/
wget https://docs.continuum.io/anaconda/hashes/Anaconda3-4.3.1-Linux-x86_64.sh-hash
wget https://repo.continuum.io/archive/Anaconda3-4.3.1-Linux-x86_64.sh
# 4447b93d2c779201e5fb50cfc45de0ec96c3804e7ad0fe201ab6b99f73e90302 sha256
# 9209864784250d6855886683ed702846 md5
sh Anaconda3-4.3.1-Linux-x86_64.sh -b -p /BGA2017/anaconda3
```
2) create the modulefile
```
wget -O /BGA2017/modulefiles/anaconda3 https://gitlab.pasteur.fr/tru/BGA2017/raw/master/noc-auth/BGA2017/modulefiles/anaconda3
```
3) update and add more packages
```
module use /BGA2017/modulefiles
module add anaconda3
conda update -y conda
conda update -y --all
conda install biopython
```
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