Impossible to launch UMI_tools

[baliaga31]

Hi,

I tried to install umi_tools with this command line:

conda install -c bioconda -c conda-forge umi_tools

which return:

`Collecting package metadata (current_repodata.json): done Solving environment: done

All requested packages already installed.

When I tried to doumi_tools --help`, I obtained this error answer:

Traceback (most recent call last): File "/home/my_computer/miniconda3/envs/snakemake/bin/umi_tools", line 5, in <module> from pkg_resources import load_entry_point File "/home/my_computer/miniconda3/envs/snakemake/lib/python3.9/site-packages/pkg_resources/__init__.py", line 3243, in <module> def _initialize_master_working_set(): File "/home/my_computer/miniconda3/envs/snakemake/lib/python3.9/site-packages/pkg_resources/__init__.py", line 3226, in _call_aside f(*args, **kwargs) File "/home/my_computer/miniconda3/envs/snakemake/lib/python3.9/site-packages/pkg_resources/__init__.py", line 3255, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/home/my_computer/miniconda3/envs/snakemake/lib/python3.9/site-packages/pkg_resources/__init__.py", line 568, in _build_master ws.require(__requires__) File "/home/my_computer/miniconda3/envs/snakemake/lib/python3.9/site-packages/pkg_resources/__init__.py", line 886, in require needed = self.resolve(parse_requirements(requirements)) File "/home/my_computer/miniconda3/envs/snakemake/lib/python3.9/site-packages/pkg_resources/__init__.py", line 772, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'umi-tools==0.2.3' distribution was not found and is required by the application I use conda and snakemake.

How I can fix that ?

Thank you for your help.

Benoit

[IanSudbery]

umi-tools 0.2.3 is a very old version of umi-tool. I think you are getting this becausae bioconda doesn't yet build umi-tools for python 3.9. You can test this with

conda install -c bioconda -c conda-forge umi-tools==1.1

It will probably complain that it can't do it, or it will try to install a different version of python.

I don't actually know of any reason why umi-tools shouldn't work with python 3.9, so you could try installing it a different way, starting with pip.

conda remove umi-tools pip install umi-tools

If that doesn't work, you could try downloading the code from the github, and installing by running

python setup.py install

from the code directory.

Either that, or allow conda to change to a python version that bioconda supports.

Hope that is some help.

On Mon, 26 Apr 2021 at 10:34, Benoît Aliaga @.***> wrote:

Hi,

I tried to install umi_tools with this command line:

conda install -c bioconda -c conda-forge umi_tools

which return:

`Collecting package metadata (current_repodata.json): done Solving environment: done All requested packages already installed.

When I tried to doumi_tools --help`, I obtained this error answer:

Traceback (most recent call last): File "/home/my_computer/miniconda3/envs/snakemake/bin/umi_tools", line 5, in

from pkg_resources import load_entry_point File "/home/my_computer/miniconda3/envs/snakemake/lib/python3.9/site-packages/pkg_resources/__init__.py", line 3243, in def _initialize_master_working_set(): File "/home/my_computer/miniconda3/envs/snakemake/lib/python3.9/site-packages/pkg_resources/__init__.py", line 3226, in _call_aside f(*args, **kwargs) File "/home/my_computer/miniconda3/envs/snakemake/lib/python3.9/site-packages/pkg_resources/__init__.py", line 3255, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/home/my_computer/miniconda3/envs/snakemake/lib/python3.9/site-packages/pkg_resources/__init__.py", line 568, in _build_master ws.require(__requires__) File "/home/my_computer/miniconda3/envs/snakemake/lib/python3.9/site-packages/pkg_resources/__init__.py", line 886, in require needed = self.resolve(parse_requirements(requirements)) File "/home/my_computer/miniconda3/envs/snakemake/lib/python3.9/site-packages/pkg_resources/__init__.py", line 772, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'umi-tools==0.2.3' distribution was not found and is required by the application I use conda and snakemake. How I can fix that ? Thank you for your help. Benoit — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub , or unsubscribe .

[baliaga31]

Thank you Ian for your help. I installed umi-tools (1.1.1) with pip and it worked :-)