Matplotlib Configuration Issues

User Support
1

Hello! I tried (after fixing the LANG issue) to run the “echo “backend: Agg” > ~/.config/matplotlib/matplotlibrc” command, but it doesn’t recognize it. I think the plugins are installed, and this is the message I get after running condo list:

(qiime2) MacBook-Pro-de-Malena-3:~ mae$ conda install matplotlib==1.5.1
Fetching package metadata .......
Solving package specifications: ..........

# All requested packages already installed.
# packages in environment at /Users/mae/Desktop/Shell/ENTER/envs/qiime2:
#
matplotlib                1.5.1               np111py35_0  
(qiime2) MacBook-Pro-de-Malena-3:~ mae$ conda list
# packages in environment at /Users/mae/Desktop/Shell/ENTER/envs/qiime2:
#
_nb_ext_conf              0.3.0                    py35_0  
anaconda-client           1.5.4                    py35_0  
appnope                   0.1.0                    py35_0  
arrow                     0.8.0                    py35_0    qiime2
binaryornot               0.3.0                0_ge797740    qiime2
biom-format               2.1.5                    py35_3    qiime2
cachecontrol              0.11.7                   py35_0  
click                     6.6                      py35_0  
clyent                    1.2.2                    py35_0  
cookiecutter              1.4.0                    py35_0    qiime2
cycler                    0.10.0                   py35_0  
decorator                 4.0.10                   py35_0  
entrypoints               0.2.2                    py35_0  
freetype                  2.5.5                         1  
future                    0.16.0                   py35_0  
h5py                      2.6.0               np111py35_2  
hdf5                      1.8.17                        1  
icu                       54.1                          0  
ijson                     2.3                      py35_0    qiime2
ipykernel                 4.5.0                    py35_0  
ipymd                     0.1.2                    py35_0    qiime2
ipython                   5.1.0                    py35_1  
ipython_genutils          0.1.0                    py35_0  
ipywidgets                5.2.2                    py35_0  
jinja2                    2.8                      py35_1  
jinja2-time               0.2.0                    py35_0    qiime2
jsonschema                2.5.1                    py35_0  
jupyter                   1.0.0                    py35_3  
jupyter_client            4.4.0                    py35_0  
jupyter_console           5.0.0                    py35_0  
jupyter_core              4.2.0                    py35_0  
libpng                    1.6.22                        0  
lockfile                  0.12.2                   py35_0  
markupsafe                0.23                     py35_2  
matplotlib                1.5.1               np111py35_0  
mistune                   0.7.3                    py35_1  
mkl                       11.3.3                        0  
natsort                   5.0.1                    py35_0  
nb_anacondacloud          1.2.0                    py35_0  
nb_conda                  2.0.0                    py35_0  
nb_conda_kernels          2.0.0                    py35_0  
nbconvert                 4.2.0                    py35_0  
nbformat                  4.1.0                    py35_0  
nbpresent                 3.0.2                    py35_0  
nose                      1.3.7                    py35_1  
notebook                  4.2.3                    py35_0  
numpy                     1.11.2                   py35_0  
openssl                   1.0.2j                        0  
pandas                    0.19.1              np111py35_0  
path.py                   8.2.1                    py35_0  
pexpect                   4.0.1                    py35_0  
pickleshare               0.7.4                    py35_0  
pip                       9.0.1                    py35_0  
poyo                      0.4.0                    py35_0    qiime2
prompt_toolkit            1.0.9                    py35_0  
ptyprocess                0.5.1                    py35_0  
pygments                  2.1.3                    py35_0  
pyparsing                 2.1.4                    py35_0  
pyqt                      4.11.4                   py35_4  
python                    3.5.2                         0  
python-dateutil           2.6.0                    py35_0  
python-frontmatter        0.2.1                    py35_0    qiime2
pytz                      2016.7                   py35_0  
pyyaml                    3.12                     py35_0  
pyzmq                     16.0.1                   py35_0  
q2-feature-table          0.0.6                    py35_0    qiime2
q2-types                  0.0.6                    py35_0    qiime2
q2cli                     0.0.6                    py35_0    qiime2
q2templates               0.0.6                    py35_0    qiime2
qiime                     2.0.6                    py35_0    qiime2
qt                        4.8.7                         4  
qtconsole                 4.2.1                    py35_0  
readline                  6.2                           2  
requests                  2.11.1                   py35_0  
scikit-bio                0.5.0               np111py35_0  
scipy                     0.18.1              np111py35_0  
seaborn                   0.7.1                    py35_0  
setuptools                27.2.0                   py35_0  
simplegeneric             0.8.1                    py35_1  
sip                       4.18                     py35_0  
six                       1.10.0                   py35_0  
sqlite                    3.13.0                        0  
terminado                 0.6                      py35_0  
tk                        8.5.18                        0  
tornado                   4.4.2                    py35_0  
traitlets                 4.3.1                    py35_0  
tzlocal                   1.3                      py35_0    qiime2
wcwidth                   0.1.7                    py35_0  
wheel                     0.29.0                   py35_0  
whichcraft                0.4.0                    py35_0    qiime2
widgetsnbextension        1.2.6                    py35_0  
xz                        5.2.2                         0  
yaml                      0.1.6                         0  
zlib                      1.2.8                         3  
(qiime2) MacBook-Pro-de-Malena-3:~ mae$ echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc
-bash: /Users/mae/.config/matplotlib/matplotlibrc: No such file or directory

I still can´t see my plugins, am I missing something?
Thanks for your help!

2

Hi @malenaamer! Are you running QIIME 2 on a server somewhere that doesn’t have a display attached to it? If not, you don’t need to worry about the echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc command. If you are installing QIIME 2 in a headless environment (no display, e.g. desktop GUI), then you need to make sure that the necessary directories are in place before running that command:

$ mkdir -p ~/.config/matplotlib
$ echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc

Hope that helps!

3

Hi Matt!

I ran the code but I´m not seeing my plugins yet, I also restarted the terminal, here’s how it looks like:

MacBook-Pro-de-Malena-3:~ mae$ source activate qiime2
(qiime2) MacBook-Pro-de-Malena-3:~ mae$ qiime info
Traceback (most recent call last):
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/bin/qiime", line 6, in <module>
    sys.exit(q2cli.__main__.qiime())
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 716, in __call__
    return self.main(*args, **kwargs)
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 675, in main
    _verify_python3_env()
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/lib/python3.5/site-packages/click/_unicodefun.py", line 119, in _verify_python3_env
    'mitigation steps.' + extra)
RuntimeError: Click will abort further execution because Python 3 was configured to use ASCII as encoding for the environment.  Either run this under Python 2 or consult http://click.pocoo.org/python3/ for mitigation steps.

This system lists a couple of UTF-8 supporting locales that
you can pick from.  The following suitable locales where
discovered: af_ZA.UTF-8, am_ET.UTF-8, be_BY.UTF-8, bg_BG.UTF-8, ca_ES.UTF-8, cs_CZ.UTF-8, da_DK.UTF-8, de_AT.UTF-8, de_CH.UTF-8, de_DE.UTF-8, el_GR.UTF-8, en_AU.UTF-8, en_CA.UTF-8, en_GB.UTF-8, en_IE.UTF-8, en_NZ.UTF-8, en_US.UTF-8, es_ES.UTF-8, et_EE.UTF-8, eu_ES.UTF-8, fi_FI.UTF-8, fr_BE.UTF-8, fr_CA.UTF-8, fr_CH.UTF-8, fr_FR.UTF-8, he_IL.UTF-8, hr_HR.UTF-8, hu_HU.UTF-8, hy_AM.UTF-8, is_IS.UTF-8, it_CH.UTF-8, it_IT.UTF-8, ja_JP.UTF-8, kk_KZ.UTF-8, ko_KR.UTF-8, lt_LT.UTF-8, nl_BE.UTF-8, nl_NL.UTF-8, no_NO.UTF-8, pl_PL.UTF-8, pt_BR.UTF-8, pt_PT.UTF-8, ro_RO.UTF-8, ru_RU.UTF-8, sk_SK.UTF-8, sl_SI.UTF-8, sr_YU.UTF-8, sv_SE.UTF-8, tr_TR.UTF-8, uk_UA.UTF-8, zh_CN.UTF-8, zh_HK.UTF-8, zh_TW.UTF-8
(qiime2) MacBook-Pro-de-Malena-3:~ mae$ export LANG=en_us.UTF-8
(qiime2) MacBook-Pro-de-Malena-3:~ mae$ qiime info
System versions
Python version: 3.5.2
QIIME version: 2.0.6
q2cli version: 0.0.6

Installed plugins
No plugins are currently installed.
You can browse the official QIIME 2 plugins at https://qiime2.org

Application config directory
/Users/mae/Library/Application Support/q2cli

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

Citing QIIME 2
If you use QIIME 2 in any published work, you should cite QIIME 2 and the plugins that you used. To display the citations for QIIME and all installed plugins, run:

  qiime info --citations

(qiime2) MacBook-Pro-de-Malena-3:~ mae$ mkdir -p ~/.config/matplotlib
(qiime2) MacBook-Pro-de-Malena-3:~ mae$ echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc
(qiime2) MacBook-Pro-de-Malena-3:~ mae$ qiime info
System versions
Python version: 3.5.2
QIIME version: 2.0.6
q2cli version: 0.0.6

Installed plugins
No plugins are currently installed.
You can browse the official QIIME 2 plugins at https://qiime2.org

Application config directory
/Users/mae/Library/Application Support/q2cli

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

Citing QIIME 2
If you use QIIME 2 in any published work, you should cite QIIME 2 and the plugins that you used. To display the citations for QIIME and all installed plugins, run:

  qiime info --citations

(qiime2) MacBook-Pro-de-Malena-3:~ mae$

Any suggestions? Thank you!

4

Hi @malenaamer - as I mentioned above, it doesn't look like you need to run the following:

because it looks like you are using a Macbook, which probably means you have a monitor available (those commands are only suggested for environments without a display).

It looks like you have successfully installed the QIIME 2 framework and the CLI interface. Now you should be able to install some plugins. Putting it together with what you just posted (slightly reordered and edited):

$ source activate qiime2
$ export LANG=en_us.UTF-8
$ conda install matplotlib==1.5.1
$ conda install -c qiime2 q2-types q2-feature-table

Now when you run qiime info you should see two new plugins installed: q2-types and q2-feature-table. If you want to install more plugins, I suggest that you follow along with the documentation. Thanks!

5

Hi matt, I´m sorry for this trouble, but I still can´t see my plugins, even after I restart and put all those commands:

Last login: Wed Dec 14 15:52:56 on ttys000
MacBook-Pro-de-Malena-3:~ mae$ source activate qiime2
(qiime2) MacBook-Pro-de-Malena-3:~ mae$ export LANG=en_us.UTF-8
(qiime2) MacBook-Pro-de-Malena-3:~ mae$ conda install matplotlib==1.5.1
Fetching package metadata .......
Solving package specifications: ..........

# All requested packages already installed.
# packages in environment at /Users/mae/Desktop/Shell/ENTER/envs/qiime2:
#
matplotlib                1.5.1               np111py35_0  
(qiime2) MacBook-Pro-de-Malena-3:~ mae$ conda install -c qiime2 q2-types q2-feature-table
Fetching package metadata .........
Solving package specifications: ..........

# All requested packages already installed.
# packages in environment at /Users/mae/Desktop/Shell/ENTER/envs/qiime2:
#
q2-feature-table          0.0.6                    py35_0    qiime2
q2-types                  0.0.6                    py35_0    qiime2
(qiime2) MacBook-Pro-de-Malena-3:~ mae$ qiime info
System versions
Python version: 3.5.2
QIIME version: 2.0.6
q2cli version: 0.0.6

Installed plugins
No plugins are currently installed.
You can browse the official QIIME 2 plugins at https://qiime2.org

Application config directory
/Users/mae/Library/Application Support/q2cli

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

Citing QIIME 2
If you use QIIME 2 in any published work, you should cite QIIME 2 and the plugins that you used. To display the citations for QIIME and all installed plugins, run:

  qiime info --citations

(qiime2) MacBook-Pro-de-Malena-3:~ mae$ qiime feature-table
Usage: qiime [OPTIONS] COMMAND [ARGS]...

Error: No such command "feature-table".
(qiime2) MacBook-Pro-de-Malena-3:~ mae$

Thanks for your help!

6

How about running qiime dev refresh-cache? That will force qiime to relearn about any plugins you have installed. Then you could run qiime info and confirm that they are registering correctly.

1 Like
7

YEEEESSS!! It worked! Thanks so much!

1 Like