squire requires two conflicting python versions? about squire HOT 1 OPEN

Hi,

I'm trying to install squire in a conda venv. I've installed all dependencies and am left with the following conflict. When I install python 2.7 then try conda install -c bioconductor squire, the error is that it requires python3. But when I install python3 then repeat, it says squire requires python 2.7. Since others have properly installed squire I'm hoping this is a simple fix. Just having trouble figuring it out. Any help is very appreciated.

I've pasted the commands and errors below.

Step 1: Install python 2.7

conda install python=2.7 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: done

conda install -c bioconda squire Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

• squire -> python[version='3.4.|3.5.|3.6.*']

Your python: python=2.7

############## Step 2: Install python 3

conda install python=3 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: done

conda install -c bioconda squire Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

• squire -> python=2.7

Your python: python=3

Hi @saralinker ,
I am also using the SQuIRE to do some analyses. My experience is that combining a little bit code modifying and version switching you can get things running smoothly.
For Fetch.py you probably want to use python2. Also remove the line 411, 412 and 413, these lines remove some temporary files which are then used, which create error.
For Clean.py you can use either python2 or python3, as long as you can install the python library dependencies such as Pyfaidx. If you select to use python3 like I do, replace the "iteritems" by "items" since iteritems are from python2.
For Count.py I have it run well on python2, I haven't tried to run it on python3 yet.

from squire.