umi_tools whitelist --help: ImportError: No module named Utilities

[madaojjc]

I installed umi_tools by

git clone https://github.com/CGATOxford/UMI-tools.git
pip install -r requirements.txt
python setup.py install

and after that, when I run umi_tools , there was no problem, but when run umi_tools whitelist --help, it showed:

UMI-Tools: Version 1.0.0
Traceback (most recent call last):
File "/usr/local/bin/umi_tools", line 11, in
load_entry_point('umi-tools==1.0.0', 'console_scripts', 'umi_tools')()
File "/home/shen/.local/lib/python2.7/site-packages/umi_tools-1.0.0-py2.7-linux-x86_64.egg/umi_tools/umi_tools.py", line 58, in main
module = importlib.import_module("umi_tools." + command, "umi_tools")
File "/usr/lib/python2.7/importlib/init.py", line 37, in import_module
import(name)
File "/home/shen/.local/lib/python2.7/site-packages/umi_tools-1.0.0-py2.7-linux-x86_64.egg/umi_tools/whitelist.py", line 205, in
import umi_tools.Utilities as U
ImportError: No module named Utilities

[madaojjc]

I tried pip install and conda, but there was still such a problem...

[IanSudbery]

Hi,

As of this new version, 1.0.0 we no longer support python 2.7. Try creating a new python 3 conda environment and installing UMI-Tools with:

conda create -n umi_tools_env -c bioconda python=3.7 umi_tools 
source activate umi_tools_env

Alternatively, if you really need to install UMI-Tools in a python 2 enviornment, please install version 0.5.5 with conda install umi_tools==0.5.5 or pip install umi_tools==0.5.5

[madaojjc]

Hi,

As of this new version, 1.0.0 we no longer support python 2.7. Try creating a new python 3 conda environment and installing UMI-Tools with:

conda create -n umi_tools_env -c bioconda python=3.7 umi_tools 
source activate umi_tools_env

Alternatively, if you really need to install UMI-Tools in a python 2 enviornment, please install version 0.5.5 with conda install umi_tools==0.5.5 or pip install umi_tools==0.5.5

Creating a new python 3 conda environment sovled my problem! THANKS A LOT!

[madaojjc]

It works! THANKS A LOT At 2019-02-17 22:39:02, "Ian Sudbery" <[email protected]> wrote: Hi, As of this new version, 1.0.0 we no longer support python 2.7. Try creating a new python 3 conda environment and installing UMI-Tools with: conda create -n umi_tools_env -c bioconda python=3.7 umi_tools source activate umi_tools_env Alternatively, if you really need to install UMI-Tools in a python 2 enviornment, please install version 0.5.5 with conda install umi_tools==0.5.5 or pip install umi_tools==0.5.5 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[IanSudbery]

Your welcome.

[qicaibiology]

Hi,

As of this new version, 1.0.0 we no longer support python 2.7. Try creating a new python 3 conda environment and installing UMI-Tools with:

conda create -n umi_tools_env -c bioconda python=3.7 umi_tools 
source activate umi_tools_env

Alternatively, if you really need to install UMI-Tools in a python 2 enviornment, please install version 0.5.5 with conda install umi_tools==0.5.5 or pip install umi_tools==0.5.5

conda install umi_tools==0.5.5 also works!