h5py installation has not completed and got error.

[WT]

Dear all,

Initially, I would like to install h5py (http://docs.h5py.org/en/latest/build.html) because h5py has not installed in my qiime 1.9.1. I followed the h5py installation guide and something went wrong.
And I get this when I test print_qiime_config.py,


Traceback (most recent call last):
  File "/usr/local/bin/print_qiime_config.py", line 44, in <module>
    from qiime.util import (load_qiime_config,
  File "/usr/local/lib/python2.7/dist-packages/qiime/util.py", line 41, in <module>
    from biom.util import compute_counts_per_sample_stats, biom_open, HAVE_H5PY
  File "/usr/local/lib/python2.7/dist-packages/biom/__init__.py", line 51, in <module>
    from .table import Table
  File "/usr/local/lib/python2.7/dist-packages/biom/table.py", line 188, in <module>
    from biom.util import (get_biom_format_version_string,
  File "/usr/local/lib/python2.7/dist-packages/biom/util.py", line 26, in <module>
    H5PY_VLEN_UNICODE = h5py.special_dtype(vlen=unicode)
  File "h5t.pyx", line 1437, in h5py.h5t.special_dtype (h5py/h5t.c:11775)
NotImplementedError: Only byte-string vlens are currently supported


Now I cannot create biom files and everything is now crap. Could you help me to reinstall back to normal or install h5py properly?

Appreciate your kind help.

Best regards,
Wei Thwe

[Colin Brislawn]

Hello Wei,

Sorry your software environments got messed up. Managing python software can be a real mess.

You have probably already figured this out, but I wanted to suggest installing these software packages again, using different conda environments. The idea here is to install qiime into a fresh conda environment, then install the version of h5py into a different conda environment. Like

conda create -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda

conda create -n newpython h5py 

So you can use qiime by running 

source activate qiime1

but then you can run h5py by running

source deactivate

source activate newpython

Let me know if this works for you,

Colin

[WT]

Dear Colin (@Colin Brislawn),

Thanks for your reply. Sorry for late reply. I have never tried the one you suggested. Let me ask you how to install conda at Terminal since it was said "conda command not found".

Appreciate your answer.

Best regards,
Wei Thwe

[Colin Brislawn]

Hello Wei Thwe,

Of course. The full instructions for installing Qiime 1 using conda are on this page: 

http://qiime.org/install/install.html#step-1-install-miniconda  

After Step 1: Install Miniconda, you can run the conda commands I posted above.

Let me know if you have any questions!

Colin

[WT]

Dear Colin,

Thanks for your reply. I managed to install "Miniconda2-latest-Linux-x86_64.sh" in my home/user.. Once I installed in my terminal, I could not proceed to your above commands. I kept on getting conda: command not found while I run the following:

WT@48LVY42:~/miniconda2$ conda create -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda
conda:command not found

May be I do not know where I should keep and install
"Miniconda2-latest-Linux-x86_64.sh"!
How could I proceed?

Thank you.

Best regards,
Wei Thwe

[Colin Brislawn]

Hello Wei Thwe,

After you download the file, you can install by running 

bash Miniconda2-latest-MacOSX-x86_64.sh

in the folder in which you placed it. After that command runs, try running the 'conda create' command again. 

Let me know if this works!

Colin

[WT]

Hi Colin,

I have installed in the place where Miniconda2-latest-Linux-x86_

64.sh is however, I typed bash command in the terminal and I received the followings.

WT@48LVY42:~/miniconda2$ bash Miniconda2-latest-Linux-x86_64.sh
ERROR: File or directory already exists: '/home/WT/miniconda2'
If you want to update an existing installation, use the -u option.

WT@48LVY42:~/miniconda2$ conda create -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda
conda: command not found

I am not sure what is missing.

[Colin Brislawn]

Hello again,

I think you have done everything right. I'm not sure what's going wrong. 

Maybe if you installed miniconda 3, this would avoid this issue. Miniconda 3 will still work with Qiime 1, but it will also work great for Qiime 2 if you want to try the newer version of Qiime in the future.

Maybe another person on the forums has an idea, because just installing miniconda 3 is my only idea.

Let me know if you find the solution,

Colin