Commit e58b36c0 authored by BIOPZ-Schmidt Ralf's avatar BIOPZ-Schmidt Ralf

updated python3 env install procedure

parent 6408baf5
......@@ -30,6 +30,21 @@ On MacOS X:
```bash
conda create -n paqr_kapac -c bioconda -c ostrokach --file requirements_py3.txt
```
**Important Update**: Please not that we experienced some difficulties with some anaconda-packages which have been removed from anaconda cloud. In order to create the python3 environment please follow these steps:
```bash
conda create -n paqr_kapac -c bioconda -c ostrokach -c r -c defaults --file requirements_py3_UPDATED.txt
```
This will result in an environment without the R package "optparse". In order to install this package please run:
```bash
conda activate paqr_kapac
R
```
Now, you should find your console to be in an active R session. Here, execute:
```R
install.packages("optparse")
q()
```
If you already have a conda version with python2 installed, create the new python 3 environment like this:
```bash
conda create -n paqr_kapac -c bioconda -c ostrokach --file requirements_py3.txt python=3
......
# This file may be used to create an environment using:
# $ conda create --name tutorial --file <this file>
python=3.5.4
snakemake=3.13.0
graphviz=2.38.0
star=2.5.2a
samtools=1.3.1
bedtools=2.26.0
gzip=1.7
r-base=3.5.1
sra-tools=2.8.2
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