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biocore / DEICODE

Robust Aitchison PCA from sparse count data
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conda install in qiime2-2018.11 #20

Closed cameronmartino closed 5 years ago

cameronmartino commented 5 years ago

currently the conda-forge installation 

conda install -c conda-forge deicode

conflicts with q2-sample-classifier=2018.11.0. The next qiime2 distribution should solve this. So for now, just acknowledging it is a known issue.

mortonjt commented 5 years ago

That shouldn't be blocking. The newest env for py36 is posted : https://github.com/qiime2/environment-files

On Tue, Jan 29, 2019, 6:26 PM Cameron Martino <notifications@github.com wrote:

currently the conda-forge installation

conda install -c conda-forge deicode

conflicts with q2-sample-classifier=2018.11.0. The next qiime2 distribution should solve this. So for now, just acknowledging it is a known issue.

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cameronmartino commented 5 years ago

@mortonjt Just tested the new qiime2-2019.1 env works fine with the conda install for deicode. However, qiime2-2018.11 conda install for deicode trys to remove everything, which is pretty confusing. 

> source activate qiime2-2018.11
> conda install -c conda-forge deicode
Collecting package metadata: done
Solving environment: done

## Package Plan ##
.....

The following packages will be REMOVED:

  cutadapt-1.18-py35_0
  deblur-1.1.0-py35_0
  fragment-insertion-4.3.5-py35_0
  q2-alignment-2018.11.0-py35_0
  q2-composition-2018.11.0-py35_0
  q2-cutadapt-2018.11.0-py35_0
  q2-dada2-2018.11.0-py35_0
  q2-deblur-2018.11.0-py35_0
  q2-demux-2018.11.0-py35_0
  q2-diversity-2018.11.0-py35_0
  q2-emperor-2018.11.0-py35_0
  q2-feature-classifier-2018.11.0-py35_0
  q2-feature-table-2018.11.0-py35_0
  q2-fragment-insertion-2018.11.0-py35_0
  q2-gneiss-2018.11.0-py35_0
  q2-longitudinal-2018.11.0-py35_0
  q2-metadata-2018.11.0-py35_0
  q2-phylogeny-2018.11.0-py35_0
  q2-quality-control-2018.11.0-py35_0
  q2-quality-filter-2018.11.0-py35_0
  q2-sample-classifier-2018.11.0-py35_0
  q2-taxa-2018.11.0-py35_0
  q2-types-2018.11.0-py35_0
  q2-vsearch-2018.11.0-py35_0
  q2cli-2018.11.0-py35_0
  q2templates-2018.11.0-py35_0
  qiime2-2018.11.0-py35_0
  unifrac-0.9.2-py35h1806a49_1

Also, 

pip install deicode

works in any env I have tested (i.e. qiime2-2018>=).

cameronmartino commented 5 years ago

@mortonjt now that qiime is updated to 2019.1 in the docs, I do not think this should be a major issue anymore. I will make a note in the plugin section that the conda install only works for 2019.1>=

mortonjt commented 5 years ago

+1

On Thu, Jan 31, 2019 at 1:42 PM Cameron Martino notifications@github.com wrote:

@mortonjt https://github.com/mortonjt now that qiime is updated to 2019.1 in the docs, I do not think this should be a major issue anymore. I will make a note in the plugin section that the conda install only works for 2019.1>=

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