Entering edit mode
5.0 years ago
yueli7
▴
250
Hello, Everyone,
I was in problem of install UMI-tools.
Thanks in advancef or any help!
Best,
Yue
~/UMI-tools$ python3 setup.py install
Downloading https://pypi.io/packages/source/s/setuptools/setuptools-10.0.zip
Extracting in /tmp/tmppcs34pkj
Now working in /tmp/tmppcs34pkj/setuptools-10.0
Building a Setuptools egg in /home/li/UMI-tools
Traceback (most recent call last):
File "setup.py", line 19, in <module>
exec(init_file.read(), command_ns)
File "<string>", line 11, in <module>
File "/tmp/tmppcs34pkj/setuptools-10.0/setuptools/__init__.py", line 11, in <module>
from setuptools.extension import Extension
File "/tmp/tmppcs34pkj/setuptools-10.0/setuptools/extension.py", line 8, in <module>
from .dist import _get_unpatched
File "/tmp/tmppcs34pkj/setuptools-10.0/setuptools/dist.py", line 19, in <module>
import pkg_resources
File "/tmp/tmppcs34pkj/setuptools-10.0/pkg_resources/__init__.py", line 1655, in <module>
register_loader_type(importlib_bootstrap.SourceFileLoader, DefaultProvider)
AttributeError: module 'importlib._bootstrap' has no attribute 'SourceFileLoader'
/home/li/UMI-tools/setuptools-10.0-py3.6.egg
Traceback (most recent call last):
File "setup.py", line 8, in <module>
use_setuptools("10.0")
File "/home/li/UMI-tools/ez_setup.py", line 178, in use_setuptools
return _do_download(version, download_base, to_dir, download_delay)
File "/home/li/UMI-tools/ez_setup.py", line 129, in _do_download
_build_egg(egg, archive, to_dir)
File "/home/li/UMI-tools/ez_setup.py", line 75, in _build_egg
raise IOError('Could not build the egg.')
OSError: Could not build the egg.
What about the other options in the installation section?
The problem here is that the installer first tries to install setuptools, which it needs to do the installation. It is the installation of setuptools that is failing.
As @Wouter said, you are definitely best installing one of the pre-built options. If you don't want to go the conda route,
pip/pip3should be fine.If you want to install from source for some reason, you'll probably need to install setuptools manually first. To do this download setuptools from: https://pypi.org/project/setuptools/
then unzip the package, and run:
$ python setup.py install --userHello, WouterDeCoster and i.sudbery,
Thank you so much for both of yours suggestions.
It seems successfully installed.
How I can use this software?
Thank you again for your great help!
Best,
Yue
Hello,
It seems successfully installed. I have no idea how to use it. Thank you!
Yue
umi-toolshas complete documentation available here. That is where you will find information on how to use the tools.Hello, genomax,
Thank you so much for your quick response!
Is that possible I can confirm I successfully installed?
Thanks in advance for your great help!
Best,
Yue
What output do you get from
which umi_tools?Hello, genomax,
Thank you so much for your great help!
So basically if
umi-toolsdid get installed it is not in your$PATHso it can't be found. Is the executable inls ~/.local/binthis directory?Hello, genmax,
Thank you so much for your patient!
I cannot find umi_tools in usr/local/bin.
Thank you again!
Yue
That was not
/usr/local/bin. It is~/.local/bin(check carefully) in your own home directory.Hello, genomax,
Thank you for your reply!
I still can not find it.
There is not usr/local/bin.
Thank you again!
Best,
Yue
For third and final time please copy and paste following command exactly as typed below
and tell us what it says.
Hello, genomax,
Thank you so much for your great help!
I finally found it!
Thank you again!
A quick question is how I can use umi_tools this software?
directories that start with
., like.localare hidden. To see them you need to dols -a.