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users:catalogue:programs:qiime2

Qiime2

As you can read in their own web, Qiime1 is no longer supported at this time. We have already installed Qiime2 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
users/catalogue/programs/qiime2.txt · Last modified: 2018/06/18 11:24 by admins_ceab