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biocore / qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
GNU General Public License v2.0
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Create QIIME package for anaconda #1759

Closed ElDeveloper closed 8 years ago

ElDeveloper commented 9 years ago

This would speed-up the installation process.

colinbrislawn commented 8 years ago

Thanks! (Sorry to ask you to take down software. I'm glad people want biocore/conda-recipes#3!)

ElDeveloper commented 8 years ago

The day will come!!!

On (Dec-03-15|13:35), Colin Brislawn wrote:

Hello everyone. This issue is being addressed over in biocore/conda-recipes/issues/3. The day will come!

@Jorge-C, could you remove your 1.9.0-dev package of qiime? I'm glad that people want to install qiime through conda, but this old build makes troubleshooting tricky.

Reply to this email directly or view it on GitHub: https://github.com/biocore/qiime/issues/1759#issuecomment-161791584

bgruening commented 8 years ago

There is now a qiime package in bioconda. Please try conda create qiime -n qiime -c bioconda. We plan to use this package for further Galaxy integration.

wasade commented 8 years ago

Thanks @bgruening! Very excited to test this out!!

ElDeveloper commented 8 years ago

Cheers @bgruening!!

bgruening commented 8 years ago

@ElDeveloper please test it if you have time. This is also a very basic QIIME, not sure if we are aiming for a full-fledged version. If we do I thought about adding a new package qiime_all that depends on qiime.

ElDeveloper commented 8 years ago

@bgruening, I just gave this a quick shot and the QIIME scripts were failing due to missing dependencies for matplotlib, this is the error message I got:

(qiime-bioconda)yoshikivazquezbaeza:~$ print_qiime_config.py -tb
Traceback (most recent call last):
  File "/Users/yoshikivazquezbaeza/miniconda/envs/qiime-bioconda/bin/print_qiime_config.py", line 4, in <module>
    __import__('pkg_resources').run_script('qiime==1.9.0rc2', 'print_qiime_config.py')
  File "/Users/yoshikivazquezbaeza/miniconda/envs/qiime-bioconda/lib/python2.7/site-packages/setuptools-20.1.1-py2.7.egg/pkg_resources/__init__.py", line 3141, in <module>
  File "/Users/yoshikivazquezbaeza/miniconda/envs/qiime-bioconda/lib/python2.7/site-packages/setuptools-20.1.1-py2.7.egg/pkg_resources/__init__.py", line 3127, in _call_aside
  File "/Users/yoshikivazquezbaeza/miniconda/envs/qiime-bioconda/lib/python2.7/site-packages/setuptools-20.1.1-py2.7.egg/pkg_resources/__init__.py", line 3154, in _initialize_master_working_set
  File "/Users/yoshikivazquezbaeza/miniconda/envs/qiime-bioconda/lib/python2.7/site-packages/setuptools-20.1.1-py2.7.egg/pkg_resources/__init__.py", line 640, in _build_master
  File "/Users/yoshikivazquezbaeza/miniconda/envs/qiime-bioconda/lib/python2.7/site-packages/setuptools-20.1.1-py2.7.egg/pkg_resources/__init__.py", line 941, in require
  File "/Users/yoshikivazquezbaeza/miniconda/envs/qiime-bioconda/lib/python2.7/site-packages/setuptools-20.1.1-py2.7.egg/pkg_resources/__init__.py", line 828, in resolve
pkg_resources.DistributionNotFound: The 'mock' distribution was not found and is required by matplotlib
(qiime-bioconda)yoshikivazquezbaeza:~$ which print_qiime_config.py 
/Users/yoshikivazquezbaeza/miniconda/envs/qiime-bioconda/bin/print_qiime_config.py

After installing mock and nose it seemed to be working.

Agree on the strategy to divide between qiime and qiime_all.

wasade commented 8 years ago

Can report that "print_qiime_config.py -t" passes on a centos 6 box in a fresh environment

On Wed, Mar 2, 2016 at 8:48 AM, Björn Grüning notifications@github.com wrote:

@ElDeveloper https://github.com/ElDeveloper please test it if you have time. This is also a very basic QIIME, not sure if we are aiming for a full-fledged version. If we do I thought about adding a new package qiime_all that depends on qiime.

— Reply to this email directly or view it on GitHub https://github.com/biocore/qiime/issues/1759#issuecomment-191321414.

wasade commented 8 years ago

@ElDeveloper, that was OSX, right?

On Wed, Mar 2, 2016 at 8:52 AM, Yoshiki Vázquez Baeza < notifications@github.com> wrote:

@bgruening https://github.com/bgruening, I just gave this a quick shot and the QIIME scripts were failing due to missing dependencies for matplotlib, this is the error message I got:

(qiime-bioconda)yoshikivazquezbaeza:~$ print_qiime_config.py -tb Traceback (most recent call last): File "/Users/yoshikivazquezbaeza/miniconda/envs/qiime-bioconda/bin/print_qiime_config.py", line 4, in import('pkg_resources').run_script('qiime==1.9.0rc2', 'print_qiime_config.py') File "/Users/yoshikivazquezbaeza/miniconda/envs/qiime-bioconda/lib/python2.7/site-packages/setuptools-20.1.1-py2.7.egg/pkg_resources/init.py", line 3141, in File "/Users/yoshikivazquezbaeza/miniconda/envs/qiime-bioconda/lib/python2.7/site-packages/setuptools-20.1.1-py2.7.egg/pkg_resources/init.py", line 3127, in _call_aside File "/Users/yoshikivazquezbaeza/miniconda/envs/qiime-bioconda/lib/python2.7/site-packages/setuptools-20.1.1-py2.7.egg/pkg_resources/init.py", line 3154, in _initialize_master_working_set File "/Users/yoshikivazquezbaeza/miniconda/envs/qiime-bioconda/lib/python2.7/site-packages/setuptools-20.1.1-py2.7.egg/pkg_resources/init.py", line 640, in _build_master File "/Users/yoshikivazquezbaeza/miniconda/envs/qiime-bioconda/lib/python2.7/site-packages/setuptools-20.1.1-py2.7.egg/pkg_resources/init.py", line 941, in require File "/Users/yoshikivazquezbaeza/miniconda/envs/qiime-bioconda/lib/python2.7/site-packages/setuptools-20.1.1-py2.7.egg/pkg_resources/init.py", line 828, in resolve pkg_resources.DistributionNotFound: The 'mock' distribution was not found and is required by matplotlib (qiime-bioconda)yoshikivazquezbaeza:~$ which print_qiime_config.py /Users/yoshikivazquezbaeza/miniconda/envs/qiime-bioconda/bin/print_qiime_config.py

After installing mock and nose it seemed to be working.

Agree on the strategy to divide between qiime and qiime_all.

— Reply to this email directly or view it on GitHub https://github.com/biocore/qiime/issues/1759#issuecomment-191322934.

bgruening commented 8 years ago

Mh, matplotlib is defined as dependency and gets installed here. Mock should be a dependency on matplotlib and I have this as well. Nose is only needed for testing, right? @wasade so it is working for you I assume?

wasade commented 8 years ago

I didn't run in detail just exercised tests. I can exercise the code further but realistically it'll be a few days before I can get to it

On Wed, Mar 2, 2016 at 8:57 AM, Björn Grüning notifications@github.com wrote:

Mh, matplotlib is defined as dependency and gets installed here. Mock should be a dependency on matplotlib and I have this as well. Nose is only needed for testing, right? @wasade https://github.com/wasade so it is working for you I assume?

— Reply to this email directly or view it on GitHub https://github.com/biocore/qiime/issues/1759#issuecomment-191324692.

ElDeveloper commented 8 years ago

@bgruening yeah, I was surprised about this. @wasade Yeah this was OSX.

colinbrislawn commented 8 years ago

@bgruening My god this works on RHEL. Well done!

(biocondaqiime)[bris469@constance03 ~]$ cat /etc/issue
Red Hat Enterprise Linux Workstation release 6.6 (Santiago)
bgruening commented 8 years ago

Nice! Next step proper Galaxy and HPC integration!

colinbrislawn commented 8 years ago

@bgruening This does not work on OSX 10.8.5. A mac version would be very useful.

WE2292:~ bris469$ conda create qiime -n biocondaqiime -c bioconda
Fetching package metadata: ........
Error: No packages found in current osx-64 channels matching: qiime
ElDeveloper commented 8 years ago

That's weird, I was testing in OSX.

On (Mar-02-16| 9:40), Colin Brislawn wrote:

@bgruening This does not work on OSX 10.8.5. A mac version would be very useful.

WE2292:~ bris469$ conda create qiime -n biocondaqiime -c bioconda
Fetching package metadata: ........
Error: No packages found in current osx-64 channels matching: qiime

Reply to this email directly or view it on GitHub: https://github.com/biocore/qiime/issues/1759#issuecomment-191344051

colinbrislawn commented 8 years ago

@bgruening I just updated my anaconda programs to make sure it was not a software version problem on my end. No luck. This currently lacks OSX support.

(root)WE2292:~ bris469$ conda create qiime -n biocondaqiime -c bioconda
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata: ........
Error: No packages found in current osx-64 channels matching: qiime

You can search for this package on anaconda.org with

    anaconda search -t conda qiime
bpenalver commented 8 years ago

I am having the same issues. It looks like the package is available for Linux but not for Mac.

gregcaporaso commented 8 years ago

I'm also not able to install on OS X. 

$ conda create qiime -n qiime-conda -c bioconda
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata: ..........
Error: No packages found in current osx-64 channels matching: qiime

Thanks so much for the work on this @bgruening and everyone else!

bgruening commented 8 years ago

@gregcaporaso @bpenalver please try again, should be available now.

colinbrislawn commented 8 years ago

This works great on OSX 10.8.5. Great work @bgruening! This is now my standard way to deploy qiime, and it works on all my *unix systems.

Can we close this issue (and then open new issue on the biocore page)?

gregcaporaso commented 8 years ago

This also worked great for me, thanks again @bgruening!