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Commit f9d1de2f authored by Mattias's avatar Mattias
Browse files

Set PATH globally

parent 10268535
......@@ -20,6 +20,11 @@ This notebook is based on the main Dada2 tutorial combined with the ITS workflow
# Getting ready
```{r setup}
Sys.setenv(PATH=paste("/opt/miniconda3/bin",Sys.getenv("PATH"),sep=":"))
```
First we load the `dada2` package If you don't already it, see the [dada2 installation instructions](dada-installation.html):
```{r libraries, message=FALSE, warning=FALSE}
library(dada2); packageVersion("dada2")
......@@ -31,7 +36,6 @@ library(Biostrings);packageVersion("Biostrings")
## Install the aspera client
```{bash}
export PATH="/opt/miniconda3/bin:$PATH"
conda create -n aspera --yes -c hcc aspera-cli
```
......@@ -130,7 +134,6 @@ These primers can be now removed using a specialized primer/adapter removal tool
Install cutadapat if you don't have it already. After installing cutadapt, we need to tell R the path to the cutadapt command.
```{bash}
export PATH="/opt/miniconda3/bin:$PATH"
conda create --yes -n cutadapt cutadapt biopython
source activate cutadapt
......@@ -143,7 +146,6 @@ We now create output filenames for the cutadapt-ed files, and define the paramet
TODO: Why are environmental values not available in the bash code chunk? PATH and PYTHONPATH need to be manually set. Also using tilde or $HOME does not work. Seems like limited bash!
```{bash}
export PATH="/opt/miniconda3/bin:$PATH"
export PYTHONPATH="/home/NIOO.INT/mattiash/.conda/envs/cutadapt/lib/python3.6/site-packages/"
source activate cutadapt
......
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