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cutadapt 安装 ubuntu

(2015-03-06 22:37:40)
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Installation

Quickstart

这里先给出下载地址吧,  用于本地的安装.

https://pypi.python.org/pypi/cutadapt/ 

The easiest way to install cutadapt is to use pip on the command line:

pip install --user cutadapt  #如果没有的话就要 安装pip http://blog.sina.com.cn/s/blog_89e084930102vhaa.html

This will download the software from PyPI (the Python packaging index), and install the cutadapt binary into $HOME/.local/bin. You can then run the program like this:

~/.local/bin/cutadapt --help

If you want to avoid typing the full path, add the directory $HOME/.local/bin to your $PATH environment variable.

If the above does not work, keep reading.

Dependencies

Cutadapt requires this software to be installed:

  • One of Python 2.6, 2.7, 3.3 or 3.4. Python 2.7 is a bit faster than the other versions.
  • A C compiler.

Under Ubuntu, you may need to install the packages build-essential and python-dev.其中的第一个我电脑自带了,第二个用sudo apt-get install python-dev安装.

Installation

If you have already downloaded and unpacked the .tar.gz file, then installation is done like this (replace "python" with "python3" to install the Python 3 version):

python setup.py install --user #一般安装的时候最好在前面加上sudo ,w我电脑在这里就装好了,跳到第一步打入
~/.local/bin/cutadapt --help 测试通过

If you get an error message:

error: command 'gcc' failed with exit status 1

Then check the entire error message. If it says something about a missing Python.h file, then you need to install the Python development packages. The appropriate package is called python-dev in Ubuntu (or python3-dev for Python 3).

Use without installation

Build the C extension module (you can try to skip this step -- a compiled version of the module for Linux x86_64 is already included):

python setup.py build_ext -i

Then simply run the script from where it is, similar to this:

bin/cutadapt --help

If you get any errors, first try to explicitly request a specific Python version by running cutadapt like this:

python2.7 bin/cutadapt --help

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