search

skovaka / UNCALLED

Raw nanopore signal mapper that enables real-time targeted sequencing
MIT License
520 stars 44 forks source link

Installation on Ubuntu 20.04.2 #28

Open enio23 opened 3 years ago

enio23 commented 3 years ago

Hello,

I am new to working with nanopore sequencing data and I would like to try UNCALLED to map some raw public electrical signal data which I have to DNA reference. By using the following command pip3 install git+https://github.com/skovaka/UNCALLED.git --user I believe that I am able to successfully install UCALLED as I get the following:

Collecting git+https://github.com/skovaka/UNCALLED.git Cloning https://github.com/skovaka/UNCALLED.git to /tmp/pip-req-build-4gxwg_2g Running command git clone -q https://github.com/skovaka/UNCALLED.git /tmp/pip-req-build-4gxwg_2g Running command git submodule update --init --recursive -q Requirement already satisfied (use --upgrade to upgrade): uncalled==2.2 from git+https://github.com/skovaka/UNCALLED.git in ./.local/lib/python3.8/site-packages/uncalled-2.2-py3.8-linux-x86_64.egg Building wheels for collected packages: uncalled Building wheel for uncalled (setup.py) ... done Created wheel for uncalled: filename=uncalled-2.2-cp38-cp38-linux_x86_64.whl size=11639490 sha256=12580f68f59df2b4d21dcebe3dd5278e8dd545eb1bccf7309c88e2004bedf0f7 Stored in directory: /tmp/pip-ephem-wheel-cache-yjk3biym/wheels/b4/66/64/ee36746e3b4be0eea3b5c6579661fc526addfc626a5ed78e98 Successfully built uncalled

However, it seems like the 'uncalled' command is not recognized yet as while I try to run some examples I get the following: uncalled: command not found.

Please, am I missing some step in between installation and trying the examples?

Any help would be very much appreciated.

Cheers, Enio

skovaka commented 3 years ago

Try running the command ~/.local/bin/uncalled. If that works, then you could add the command export PATH=~/.local/bin:$PATH to your "~/.bashrc" file to add that directory to your system path.

If that doesn't work, try running pip3 show uncalled. For me that returns "Location: /home/skovaka/.local/lib/python3.6/site-packages", which is the location for the python package. You should be able to find the uncalled script by replacing "lib/..." with "bin/uncalled", so for me it's at /home/skovaka/.local/bin/uncalled.

Hope that helps!