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mdshw5 / pyfaidx

Efficient pythonic random access to fasta subsequences
https://pypi.python.org/pypi/pyfaidx
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question about installation #107

Closed Vivianstats closed 7 years ago

Vivianstats commented 7 years ago

Hello,

I have installed faidx using pip install --user pyfaidx and got the following results:

Downloading/unpacking pyfaidx Downloading pyfaidx-0.4.8.1.tar.gz Running setup.py (path:/tmp/pip_build_liwei92/pyfaidx/setup.py) egg_info for package pyfaidx

warning: no files found matching 'docs/build/html/*'

Requirement already satisfied (use --upgrade to upgrade): six in /usr/local/lib/python2.7/dist-packages (from pyfaidx) Requirement already satisfied (use --upgrade to upgrade): setuptools>=0.7 in /usr/local/lib/python2.7/dist-packages (from pyfaidx) Installing collected packages: pyfaidx Running setup.py install for pyfaidx

warning: no files found matching 'docs/build/html/*'
Installing faidx script to /home/liwei92/.local/bin

Could not find .egg-info directory in install record for pyfaidx Successfully installed pyfaidx Cleaning up...

But when I tried to use it in command lines with faidx --split-files example.fa, it says

faidx: command not found

Am I missing something? I appreciate it if anyone can help.

mdshw5 commented 7 years ago

No worries. You should add /home/liwei92/.local/bin to your $PATH environment variable:

PATH=$PATH:/home/liwei92/.local/bin

You can add that line to your ~/.bashrc file so the change is persistent between logins. You can find more information here: http://unix.stackexchange.com/questions/26047/how-to-correctly-add-a-path-to-path

The TLDR is that $PATH is where your shell looks for programs it can execute, so when you type faidx, bash will find /home/liwei92/.local/bin/faidx.