## Qiime2

As you can read in [their own web](http://qiime.org), Qiime1 is no longer supported at this time. We have already installed [Qiime2](http://qiime2.org) instead.

We think that is more easy to use qiime2 than qiime1:

### Interactive session with qiime2

Open a session with qlogin and the first thing you would do is:

```
xavier.roijals@node101:~$ export LANG=es_ES.UTF-8
```
(This is to solve an error with the system locale). Next step is:

```
xavier.roijals@node101:~$ source /home/soft/miniconda2/bin/activate /home/soft/miniconda2/envs/qiime2-2018.2
```
With this command, you have already activated a python virtualenv with qiime2.

If you want to see that qiime2 is already running:

```
(/home/soft/miniconda2/envs/qiime2-2018.2) xavier.roijals@node101:~$ qiime --help
Usage: qiime [OPTIONS] COMMAND [ARGS]...

  QIIME 2 command-line interface (q2cli)
  --------------------------------------

  To get help with QIIME 2, visit https://qiime2.org.

  To enable tab completion in Bash, run the following command or add it to
  your .bashrc/.bash_profile:

      source tab-qiime

  To enable tab completion in ZSH, run the following commands or add them to
  your .zshrc:

      autoload bashcompinit && bashcompinit && source tab-qiime

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.
(...)
```

### Sending a job with qsub

You can use this script as a example, changing the line qiime --help for the command you want to use.


```
#!/bin/bash

# mandatory export
# you can use the locale you want
export LANG=ca_ES.UTF-8

# activate virtualenv
source /home/soft/miniconda2/bin/activate /home/soft/miniconda2/envs/qiime2-2018.2

qiime --help > ajuda_del_qiime.txt # this is the line you must change.

deactivate
```