---
# System prepended metadata

title: Notes for Adesola

---

# Notes for Adesola

## Using rMAP on ARC4

After installing the conda environment we need to activate the environment to enter into it so we can use the installed software.

```bash=
$ source activate rMAP-1.0

(rMAP-1.0) $ 
```

### Creating a directory

```bash=
$ mkdir exp_inputs

# to move all the fastq files to the exp_inputs folder
$ mv Sal01_S39_*.fastq* exp_inputs
```

### Next steps

Log back onto ARC4, run all this from your home directory.

```bash=
$ source activate rMAP-1.0

# install dependencies 
(rMAP-1.0) $ rMAP/bin/rMAP -t 8 -c

# to do a test run
(rMAP-1.0) $ rMAP/bin/rMAP -t 8 --reference salreference.gb \
--input testsal --output salresult \
--quality --assembly shovill --amr \
--varcall --trim --phylogeny --pangenome --gen-ele
```