'extract' is not a UMI-tools command.

[yueli8]

Hello,

It looks like that I have already installed UMI-tools, but extractdoes not work.

Thank you in advance for your great help!

Best,

Yue

-P330:~/UMI-tools-master$ umi_tools
For full UMI-tools documentation, see: https://umi-tools.readthedocs.io/en/latest/

umi_tools.py - Tools for UMI analyses
=====================================

:Author: Tom Smith & Ian Sudbury, CGAT
:Tags: Genomics UMI

There are 6 tools:

  - whitelist
  - extract
  - group
  - dedup
  - count
  - count_tab

To get help on a specific tool, type:

    umi_tools <tool> --help

To use a specific tool, type::

    umi_tools <tool> [tool options] [tool arguments]

-P330:~/UMI-tools-master$ umi_tools extract
'extract' is not a UMI-tools command. See 'umi_tools -h'.

For full UMI-tools documentation, see: https://umi-tools.readthedocs.io/en/latest/

umi_tools.py - Tools for UMI analyses
=====================================

:Author: Tom Smith & Ian Sudbury, CGAT
:Tags: Genomics UMI

There are 6 tools:

  - whitelist
  - extract
  - group
  - dedup
  - count
  - count_tab

To get help on a specific tool, type:

    umi_tools <tool> --help

To use a specific tool, type::

    umi_tools <tool> [tool options] [tool arguments]

[IanSudbery]

This means that the PYTHONPATH isn't setup to look in the place where umi-tools is install.

I looked at the install log you posted a minute ago, and this caught my eye:

umi-tools 1.1.5 is already the active version in easy-install.pth

I wonder if its still looking in the python 2 location?

what do you get if you do

$ cat `which umi_tools`

[yueli8]

Hello IanSudbery,

Thank you so much for your quick response!

1. It seems that I have alredy installed umi_tools in /home/yueli/.local/bin/umi_tools.

P330:~$ which umi_tools
/home/yueli/.local/bin/umi_tools

2. Is that because I installed python 3.8 not python 3.7?

   P330:~$ pip3 --version
   pip 24.0 from /home/yueli/.local/lib/python3.8/site-packages/pip (python 3.8)

3. 'extract' is not a UMI-tools command in $ path

Thank you again and really appreciated your great help!

Best,

Yue

P330:~$ umi_tools
For full UMI-tools documentation, see: https://umi-tools.readthedocs.io/en/latest/

umi_tools.py - Tools for UMI analyses
=====================================

:Author: Tom Smith & Ian Sudbury, CGAT
:Tags: Genomics UMI

There are 6 tools:

  - whitelist
  - extract
  - group
  - dedup
  - count
  - count_tab

To get help on a specific tool, type:

    umi_tools <tool> --help

To use a specific tool, type::

    umi_tools <tool> [tool options] [tool arguments]

yueli@yueli-ThinkStation-P330:~$ umi_tools extract
'extract' is not a UMI-tools command. See 'umi_tools -h'.

For full UMI-tools documentation, see: https://umi-tools.readthedocs.io/en/latest/

umi_tools.py - Tools for UMI analyses
=====================================

:Author: Tom Smith & Ian Sudbury, CGAT
:Tags: Genomics UMI

There are 6 tools:

  - whitelist
  - extract
  - group
  - dedup
  - count
  - count_tab

To get help on a specific tool, type:

    umi_tools <tool> --help

To use a specific tool, type::

    umi_tools <tool> [tool options] [tool arguments]

[IanSudbery]

Python 3.7 vs 3.8 shouldn't make any difference. However, UMI-tools will be linked to the python installed when it is installed. The "sheband" line at the start of the /home/yueli/.local/bin/umi_tools script will indicate which python it is trying to run from.