pip install returning scikit-bio error

After installing the latest version of Qiime (2023.2) into a conda environment using the yml file, when I then pip install q2-greengenes2 I get the following error:

 gcc -pthread -B /opt/apps/apps/binapps/anaconda3/2022.10/compiler_compat -shared -Wl,-rpath,/opt/apps/apps/binapps/anaconda3/2022.10/lib -Wl,-rpath-link,/opt/apps/apps/binapps/anaconda3/2022.10/lib -L/opt/apps/apps/binapps/anaconda3/2022.10/lib -L/opt/apps/apps/binapps/anaconda3/2022.10/lib -Wl,-rpath,/opt/apps/apps/binapps/anaconda3/2022.10/lib -Wl,-rpath-link,/opt/apps/apps/binapps/anaconda3/2022.10/lib -L/opt/apps/apps/binapps/anaconda3/2022.10/lib build/temp.linux-x86_64-cpython-39/skbio/stats/__subsample.o -o build/lib.linux-x86_64-cpython-39/skbio/stats/__subsample.cpython-39-x86_64-linux-gnu.so
  building 'skbio.alignment._ssw_wrapper' extension
  creating build/temp.linux-x86_64-cpython-39/skbio/alignment
  creating build/temp.linux-x86_64-cpython-39/skbio/alignment/_lib
  gcc -pthread -B /opt/apps/apps/binapps/anaconda3/2022.10/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /opt/apps/apps/binapps/anaconda3/2022.10/include -I/opt/apps/apps/binapps/anaconda3/2022.10/include -fPIC -O2 -isystem /opt/apps/apps/binapps/anaconda3/2022.10/include -fPIC -I/tmp/pip-build-env-m6t9485v/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-build-env-m6t9485v/overlay/lib/python3.9/site-packages/numpy/core/include -I/opt/apps/apps/binapps/anaconda3/2022.10/include/python3.9 -c skbio/alignment/_lib/ssw.c -o build/temp.linux-x86_64-cpython-39/skbio/alignment/_lib/ssw.o -I. -fopenmp-simd -DSIMDE_ENABLE_OPENMP
  gcc: error: unrecognized command line option '-fopenmp-simd'
  error: command '/usr/bin/gcc' failed with exit code 1
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for scikit-bio Failed to build scikit-bio ERROR: Could not build wheels for scikit-bio, which is required to install pyproject.toml-based projects

And if I then run qiime --help I don't see the q2-greengenes2 plugin so I guess it hasn't installed correctly. Do you have any advice on this please? Thank you

Hi @elayton13, that is certainly unexpected. I'm surprised q2-greengenes2 is attempting to install skbio as it will already be there from the broader Q2 environment.

Just to verify, was pip install q2-greengenes2 performed within the QIIME 2 2023.2 conda environment? The error output here suggests, if I read this right, that the error is relative to a 2022.10 environment

Hi @wasade thanks for getting back to me so quickly. Yes I created the qiime 2023.2 environment with: conda env create -n qiime2-2023.2 --file qiime2-2023.2-py38-linux-conda.yml then activated the environment, typed qiime to see the manual page and verify it installed correctly, then ran pip install q2-greengenes2. I'm pretty sure 2022.10 is only referring to the anaconda version that I have loaded (I'm working on a HPC facility).

I tried creating a new env with qiime2.2022.8 as you describe this version on the homepage for this tool. This time the pip install seems to have worked: Successfully installed nltk-3.8.1 q2-greengenes2-2023.3 redbiom-0.3.9 regex-2023.3.2 However, if I type: qiime greengenes2 I get: Error: QIIME 2 has no plugin/command named 'greengenes2'

And I also don't see it on the qiime manual page. Do you have any ideas about what might be going wrong here? Thanks for the help

Hi @elayton13, sorry for the slow reply, I've been offline for a few days. Can you provide the output from the following commands?

$ conda activate qiime2-2023.2
$ conda list
$ pip install q2-greengenes2
$ python -c "import q2_gg2; print(q2_gg2.__file__)"
$ python -c "import qiime2; print(qiime2.__file__)"

No worries. I'll attach a txt file for the output of conda list. Actually this time pip install q2-greengenes had the following output which I didn't get before. ERROR: Could not install packages due to an OSError: [Errno 13] Permission denied: 'PKG-INFO' Consider using the --user option or check the permissions.

And when I used the --user option it seems to have worked:

Collecting q2-greengenes2 Using cached q2_greengenes2-2023.3-py3-none-any.whl Collecting scikit-bio Using cached scikit_bio-0.5.8-cp39-cp39-linux_x86_64.whl Collecting iow Using cached iow-1.0.6-cp39-cp39-linux_x86_64.whl Collecting biom-format Using cached biom_format-2.1.14-cp39-cp39-linux_x86_64.whl Collecting redbiom Using cached redbiom-0.3.9-py3-none-any.whl Requirement already satisfied: numpy>=1.9.2 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from biom-format->q2-greengenes2) (1.21.5) Requirement already satisfied: scipy>=1.3.1 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from biom-format->q2-greengenes2) (1.9.1) Requirement already satisfied: click in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from biom-format->q2-greengenes2) (8.0.4) Requirement already satisfied: cython in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from biom-format->q2-greengenes2) (0.29.32) Requirement already satisfied: h5py in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from biom-format->q2-greengenes2) (3.7.0) Requirement already satisfied: pandas>=0.20.0 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from biom-format->q2-greengenes2) (1.4.4) Requirement already satisfied: nose>=1.3.7 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from iow->q2-greengenes2) (1.3.7) Collecting hdmedians>=0.14.1 Using cached hdmedians-0.14.2-cp39-cp39-linux_x86_64.whl Collecting pandas>=0.20.0 Using cached pandas-2.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.4 MB) Collecting natsort>=4.0.3 Using cached natsort-8.3.1-py3-none-any.whl (38 kB) Requirement already satisfied: IPython>=3.2.0 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from scikit-bio->q2-greengenes2) (7.31.1) Requirement already satisfied: decorator>=3.4.2 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from scikit-bio->q2-greengenes2) (5.1.1) Collecting lockfile>=0.10.2 Using cached lockfile-0.12.2-py2.py3-none-any.whl (13 kB) Collecting CacheControl>=0.11.5 Using cached CacheControl-0.12.11-py2.py3-none-any.whl (21 kB) Requirement already satisfied: matplotlib>=1.4.3 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from scikit-bio->q2-greengenes2) (3.5.2) Requirement already satisfied: requests in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from redbiom->q2-greengenes2) (2.28.1) Requirement already satisfied: joblib in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from redbiom->q2-greengenes2) (1.1.0) Requirement already satisfied: msgpack in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from redbiom->q2-greengenes2) (1.0.3) Requirement already satisfied: nltk in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from redbiom->q2-greengenes2) (3.7) Requirement already satisfied: pygments in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (2.11.2) Requirement already satisfied: backcall in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.2.0) Requirement already satisfied: pexpect>4.3 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (4.8.0) Requirement already satisfied: traitlets>=4.2 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (5.1.1) Requirement already satisfied: jedi>=0.16 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.18.1) Requirement already satisfied: pickleshare in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.7.5) Requirement already satisfied: matplotlib-inline in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.1.6) Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (3.0.20) Requirement already satisfied: setuptools>=18.5 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (63.4.1) Requirement already satisfied: pyparsing>=2.2.1 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (3.0.9) Requirement already satisfied: fonttools>=4.22.0 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (4.25.0) Requirement already satisfied: cycler>=0.10 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (0.11.0) Requirement already satisfied: packaging>=20.0 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (21.3) Requirement already satisfied: kiwisolver>=1.0.1 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (1.4.2) Requirement already satisfied: python-dateutil>=2.7 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (2.8.2) Requirement already satisfied: pillow>=6.2.0 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (9.2.0) Requirement already satisfied: pytz>=2020.1 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from pandas>=0.20.0->biom-format->q2-greengenes2) (2022.1) Collecting tzdata>=2022.1 Using cached tzdata-2023.3-py2.py3-none-any.whl (341 kB) Requirement already satisfied: regex>=2021.8.3 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from nltk->redbiom->q2-greengenes2) (2022.7.9) Requirement already satisfied: tqdm in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from nltk->redbiom->q2-greengenes2) (4.64.1) Requirement already satisfied: charset-normalizer<3,>=2 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from requests->redbiom->q2-greengenes2) (2.0.4) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from requests->redbiom->q2-greengenes2) (1.26.11) Requirement already satisfied: certifi>=2017.4.17 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from requests->redbiom->q2-greengenes2) (2022.9.14) Requirement already satisfied: idna<4,>=2.5 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from requests->redbiom->q2-greengenes2) (3.3) Requirement already satisfied: parso<0.9.0,>=0.8.0 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from jedi>=0.16->IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.8.3) Requirement already satisfied: ptyprocess>=0.5 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from pexpect>4.3->IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.7.0) Requirement already satisfied: wcwidth in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.2.5) Requirement already satisfied: six>=1.5 in /opt/apps/apps/binapps/anaconda3/2022.10/lib/python3.9/site-packages (from python-dateutil>=2.7->matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (1.16.0) Installing collected packages: lockfile, tzdata, natsort, hdmedians, pandas, CacheControl, scikit-bio, biom-format, redbiom, iow, q2-greengenes2 Successfully installed CacheControl-0.12.11 biom-format-2.1.14 hdmedians-0.14.2 iow-1.0.6 lockfile-0.12.2 natsort-8.3.1 pandas-2.0.1 q2-greengenes2-2023.3 redbiom-0.3.9 scikit-bio-0.5.8 tzdata-2023.3

python -c "import q2_gg2; print(q2_gg2.file)" Traceback (most recent call last): File "", line 1, in ModuleNotFoundError: No module named 'q2_gg2'

and python -c "import qiime2; print(qiime2.file)" Traceback (most recent call last): File "", line 1, in ModuleNotFoundError: No module named 'qiime2'

I still don't see it when I type qiime or qiime greengenes-2.

conda_list.txt

Great thanks. So I think the main issue is that a centralized version of conda is being used, and that is leading to issues installing additional packages.

First, it looks as though qiime2 is not actually in your environment after activation, which is certainly unexpected as you've indicated that running qiime does work. You should see something qualitatively similar to the following when doing the print in the QIIME 2 import hence the confusion:

$ python -c "import qiime2; print(qiime2.__file__)"
/Users/dtmcdonald/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/__init__.py

What would explain this is if your conda environment is using a different Python binary. If so, it may also be using a different pip, which would definitely disrupt installation of additional libraries.

Can you send the output of the following?

$ which qiime
$ which python
$ which python3
$ which pip
$ which pip3

Second, I strongly suspect pip --user ... does not interact correctly with conda. If the wrong pip is being used, and we can account for that, the it may be that libraries can be installed. However, I don't really know as if you're using a central conda then you won't have write permissions to modify that environment.

I've always found centralized conda installations to be really confusing.

Hmmm ok, yes I find it all confusing too! This is the output:

(qiime2-2023.2) [mfbx4el4@login2 [csf3] qiime_2023]$ which qiime ~/.conda/envs/qiime2-2023.2/bin/qiime (qiime2-2023.2) [mfbx4el4@login2 [csf3] qiime_2023]$ which python ~/.conda/envs/qiime2-2023.2/bin/python (qiime2-2023.2) [mfbx4el4@login2 [csf3] qiime_2023]$ which python3 ~/.conda/envs/qiime2-2023.2/bin/python3 (qiime2-2023.2) [mfbx4el4@login2 [csf3] qiime_2023]$ which pip ~/.conda/envs/qiime2-2023.2/bin/pip (qiime2-2023.2) [mfbx4el4@login2 [csf3] qiime_2023]$ which pip3 ~/.conda/envs/qiime2-2023.2/bin/pip3

Actually if I run that command I do get similar to you sorry, not sure why I didn't before (qiime2-2023.2) [mfbx4el4@login2 [csf3] qiime_2023]$ python -c "import qiime2; print(qiime2.file)" /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/init.py

but the other is the same (qiime2-2023.2) [mfbx4el4@login2 [csf3] qiime_2023]$ python -c "import q2_gg2; print(q2_gg2.file)" Traceback (most recent call last): File "", line 1, in ModuleNotFoundError: No module named 'q2_gg2'

Just to be super safe, now that the environment appears activated (e.g., the print(qiime2.__file__) works), could you try rerunning pip install q2-greengenes2? The prior pip output suggests the environment may not have been active as that print test didn't work

Also, did you create the QIIME 2 environment following the QIIME 2 installation instructions? Or was it created some otherway, or by someone else?

I was instructed to load a proxy and then to load anaconda with module load apps/binapps/anaconda3/2022.10. I then followed the qiime instructions (wget and creating the env from the .yml file)

Thanks for all your help so far! I'm also asking the core facility for assistance too. Pip install output is similar:

(qiime2-2023.2) [mfbx4el4@login2 [csf3] qiime_2023]$ pip install q2-greengenes2 Collecting q2-greengenes2 Using cached q2_greengenes2-2023.3-py3-none-any.whl Collecting redbiom Using cached redbiom-0.3.9-py3-none-any.whl Requirement already satisfied: iow in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from q2-greengenes2) (1.0.5) Requirement already satisfied: biom-format in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from q2-greengenes2) (2.1.12) Requirement already satisfied: scikit-bio in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from q2-greengenes2) (0.5.7) Requirement already satisfied: click in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from biom-format->q2-greengenes2) (8.1.3) Requirement already satisfied: h5py in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from biom-format->q2-greengenes2) (2.10.0) Requirement already satisfied: pandas>=0.20.0 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from biom-format->q2-greengenes2) (2.0.0) Requirement already satisfied: cython>=0.29 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from biom-format->q2-greengenes2) (0.29.33) Requirement already satisfied: scipy>=1.3.1 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from biom-format->q2-greengenes2) (1.8.1) Requirement already satisfied: numpy>=1.9.2 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from biom-format->q2-greengenes2) (1.23.5) Requirement already satisfied: nose>=1.3.7 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from iow->q2-greengenes2) (1.3.7) Requirement already satisfied: lockfile>=0.10.2 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from scikit-bio->q2-greengenes2) (0.12.2) Requirement already satisfied: CacheControl>=0.11.5 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from scikit-bio->q2-greengenes2) (0.12.11) Requirement already satisfied: decorator>=3.4.2 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from scikit-bio->q2-greengenes2) (4.4.2) Requirement already satisfied: IPython>=3.2.0 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from scikit-bio->q2-greengenes2) (8.10.0) Requirement already satisfied: natsort>=4.0.3 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from scikit-bio->q2-greengenes2) (8.3.0) Requirement already satisfied: hdmedians>=0.14.1 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from scikit-bio->q2-greengenes2) (0.14.2) Requirement already satisfied: matplotlib>=1.4.3 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from scikit-bio->q2-greengenes2) (3.6.0) Requirement already satisfied: scikit-learn>=0.19.1 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from scikit-bio->q2-greengenes2) (0.24.1) Collecting nltk Using cached nltk-3.8.1-py3-none-any.whl (1.5 MB) Requirement already satisfied: msgpack in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from redbiom->q2-greengenes2) (1.0.4) Requirement already satisfied: requests in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from redbiom->q2-greengenes2) (2.28.2) Requirement already satisfied: joblib in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from redbiom->q2-greengenes2) (1.2.0) Requirement already satisfied: six in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from h5py->biom-format->q2-greengenes2) (1.16.0) Requirement already satisfied: pickleshare in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.7.5) Requirement already satisfied: pexpect>4.3 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (4.8.0) Requirement already satisfied: prompt-toolkit<3.1.0,>=3.0.30 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (3.0.36) Requirement already satisfied: jedi>=0.16 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.18.2) Requirement already satisfied: stack-data in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.6.2) Requirement already satisfied: matplotlib-inline in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.1.6) Requirement already satisfied: backcall in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.2.0) Requirement already satisfied: pygments>=2.4.0 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (2.14.0) Requirement already satisfied: traitlets>=5 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from IPython>=3.2.0->scikit-bio->q2-greengenes2) (5.9.0) Requirement already satisfied: kiwisolver>=1.0.1 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (1.4.4) Requirement already satisfied: pillow>=6.2.0 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (9.2.0) Requirement already satisfied: pyparsing>=2.2.1 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (3.0.9) Requirement already satisfied: cycler>=0.10 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (0.11.0) Requirement already satisfied: fonttools>=4.22.0 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (4.38.0) Requirement already satisfied: packaging>=20.0 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (23.0) Requirement already satisfied: contourpy>=1.0.1 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (1.0.7) Requirement already satisfied: python-dateutil>=2.7 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from matplotlib>=1.4.3->scikit-bio->q2-greengenes2) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from pandas>=0.20.0->biom-format->q2-greengenes2) (2022.7.1) Requirement already satisfied: tzdata>=2022.1 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from pandas>=0.20.0->biom-format->q2-greengenes2) (2023.3) Requirement already satisfied: threadpoolctl>=2.0.0 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from scikit-learn>=0.19.1->scikit-bio->q2-greengenes2) (3.1.0) Requirement already satisfied: tqdm in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from nltk->redbiom->q2-greengenes2) (4.64.1) Collecting regex>=2021.8.3 Using cached regex-2023.3.23-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (771 kB) Requirement already satisfied: certifi>=2017.4.17 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from requests->redbiom->q2-greengenes2) (2022.12.7) Requirement already satisfied: idna<4,>=2.5 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from requests->redbiom->q2-greengenes2) (3.4) Requirement already satisfied: charset-normalizer<4,>=2 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from requests->redbiom->q2-greengenes2) (2.1.1) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from requests->redbiom->q2-greengenes2) (1.26.14) Requirement already satisfied: parso<0.9.0,>=0.8.0 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from jedi>=0.16->IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.8.3) Requirement already satisfied: ptyprocess>=0.5 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from pexpect>4.3->IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.7.0) Requirement already satisfied: wcwidth in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from prompt-toolkit<3.1.0,>=3.0.30->IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.2.6) Requirement already satisfied: pure-eval in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from stack-data->IPython>=3.2.0->scikit-bio->q2-greengenes2) (0.2.2) Requirement already satisfied: asttokens>=2.1.0 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from stack-data->IPython>=3.2.0->scikit-bio->q2-greengenes2) (2.2.1) Requirement already satisfied: executing>=1.2.0 in /mnt/fls01-home01/mfbx4el4/.conda/envs/qiime2-2023.2/lib/python3.8/site-packages (from stack-data->IPython>=3.2.0->scikit-bio->q2-greengenes2) (1.2.0) Installing collected packages: regex, nltk, redbiom, q2-greengenes2 DEPRECATION: Configuring installation scheme with distutils config files is deprecated and will no longer work in the near future. If you are using a Homebrew or Linuxbrew Python, please see discussion at https://github.com/Homebrew/homebrew-core/issues/76621 DEPRECATION: Configuring installation scheme with distutils config files is deprecated and will no longer work in the near future. If you are using a Homebrew or Linuxbrew Python, please see discussion at https://github.com/Homebrew/homebrew-core/issues/76621 WARNING: The script nltk is installed in '/mnt/fls01-home01/mfbx4el4/gridware/share/python/2.7.8/bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. DEPRECATION: Configuring installation scheme with distutils config files is deprecated and will no longer work in the near future. If you are using a Homebrew or Linuxbrew Python, please see discussion at https://github.com/Homebrew/homebrew-core/issues/76621 WARNING: The script redbiom is installed in '/mnt/fls01-home01/mfbx4el4/gridware/share/python/2.7.8/bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. DEPRECATION: Configuring installation scheme with distutils config files is deprecated and will no longer work in the near future. If you are using a Homebrew or Linuxbrew Python, please see discussion at https://github.com/Homebrew/homebrew-core/issues/76621 DEPRECATION: Configuring installation scheme with distutils config files is deprecated and will no longer work in the near future. If you are using a Homebrew or Linuxbrew Python, please see discussion at https://github.com/Homebrew/homebrew-core/issues/76621 Successfully installed nltk-3.8.1 q2-greengenes2-2023.3 redbiom-0.3.9 regex-2023.3.23

Great!!! That output shows Successfully installed nltk-3.8.1 q2-greengenes2-2023.3 redbiom-0.3.9 regex-2023.3.23. Within the activated QIIME 2 environment, does the greengenes2 plugin now show?

Yeah this is similar to the output I got when I tried the --user option, but it still doesn't show! What happens is when I do pip install after module load apps/binapps/anaconda3/2022.10 I get: lots of 'requirements already satisfied...' and then: Attempting uninstall: pandas Found existing installation: pandas 1.4.4 Uninstalling pandas-1.4.4: ERROR: Could not install packages due to an OSError: [Errno 13] Permission denied: 'PKG-INFO' Consider using the --user option or check the permissions.

but if I don't do module load apps/binapps/anaconda3/2022.10 before the pip install then I get the output in my last comment. I also got the successfully installed greengenes message when I tried making a different conda env with an earlier version of qiime. But in neither of these instances could I actually see or use the plug in despite it saying successfully installed, even after closing down my session and starting again. So it seems it is installing somewhere but I can't call on it I guess? Could that make sense?

Does it work to install other plugins? What about pip install empress? If that doesn't work, then what may be better would be if we open a thread on the QIIME 2 Forum. I have a suspicion this isn't greengenes2 specific

Yes the same thing happens! I get the same messages with and without loading the anaconda module and I still can't see or use the plug in with qiime empress and it isn't listed when I type qiime, despite returning:

Successfully built empress Installing collected packages: empress DEPRECATION: Configuring installation scheme with distutils config files is deprecated and will no longer work in the near future. If you are using a Homebrew or Linuxbrew Python, please see discussion at https://github.com/Homebrew/homebrew-core/issues/76621 WARNING: The script empress is installed in '/mnt/fls01-home01/mfbx4el4/gridware/share/python/2.7.8/bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. DEPRECATION: Configuring installation scheme with distutils config files is deprecated and will no longer work in the near future. If you are using a Homebrew or Linuxbrew Python, please see discussion at https://github.com/Homebrew/homebrew-core/issues/76621 Successfully installed empress-1.2.0

Sorry to trouble you with all of this I thought it was specific to this plug-in, seems like some sort of problem with my clusters anaconda and the plug-ins I guess? If you could help me raise it with qiime that would be great!

No worries! This stuff gets confusing quickly. Are you registered on the QIIME 2 forum? What I recommend is briefly summarizing the issue, something like "I'm using a system provided installation of Conda. I'm able to install QIIME 2 2023.2 successfully, but have been unable to install additional plugins from pip. A further description of what we've tried so far is covered in "https://github.com/biocore/q2-greengenes2/issues/16". Essentially, we can get pip to report a successful installation, however "qiime" does not appear to see the installed plugins."

My username on the form is also wasade if you'd like to tag me

Ugh, github squashed the URL to this issue. Instead of the "#16", it would be good to use the full URL to this thread

I believe this issue can be closed as it was a general plugin installation problem with QIIME 2 not q2-greengenes2 specifically. Please reopen if needed

biocore / q2-greengenes2

pip install returning scikit-bio error #16