Installing a python package/tool by a non root user
Question:
(1) I have to install one python package (HTSeq) but i dont have root privileges.
The package need python 2.4 or latest version. We have python 2.3 on our cluster.
Thus I installed python 2.7 on my one local directory
using
./configure --prefix=/home/amit/tools/localpython
make
make install
(2) The package also requires numpy : so I also installed it on my local directory using:
/home/amit/tools/localpython/bin/python2.7 setup.py install --home=/home/amit/tools/localnumpy
and done
>>> sys.path.append("/home/amit/tools/localnumpy/lib/")
(3) I downloaded the tar file of HTSeq (Which i want to download) and run
/home/amit/tools/localpython/bin/python2.7 setup.py install --home=/home/amit/tools/localhtseq
it is throwing following error:
Could not import 'setuptools',
falling back to 'distutils'.
Setup script for HTSeq: Failed to import 'numpy'.
Please install numpy and then try again to install HTSeq.
Kindly provide me some hint on how to get over it
Thanks in advance
Answers:
Setuptools is another requirement which you need to install that package.
One option is to use virtualenv to create a contained python environment. This can be made everywhere and is owned by the user who creates it.
To install virtualenv without admin rights (from this answer):
Download tar.gz of the latest version of virtualenv.
Unpack it.
You don’t even need to install it, just run virtualenv.py, for example:
wget http://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.7.1.2.tar.gz
tar -xzf virtualenv-1.7.1.2.tar.gz
/home/amit/tools/localpython/bin/python2.7 virtualenv-1.7.1.2/virtualenv.py env
env/bin/pip install HTSeq
env/bin/pip install numpy
Now run your script using the python binary in the virtual environment:
env/bin/python myscript.py
1) You have to install setuptools (it is necessary to run setup.py of your HTSeq).
Download sources tar.gz setuptools-0.6c11.tar.gz, unpack it, and then do the steps like you installed python2.7, but in the folder where you unpacked setuptools sources:
./configure --prefix=/home/amit/tools/localpython
make
make install
2) When you will install setuptools, a easy_install executable will apear in python2.7/scripts/ folder. You can use it to install packages easily:
/home/amit/tools/localpython/bin/python2.7/scripts/easy_install HTSeq
it will automatically find the package and will download and install it for you along with all dependencies.
Another way is to install pip as the local user and then install packages. As explained in the pip docs (check for OS specifics) you can install it as follows – obtain the get-pip.py script, then run it:
wget https://bootstrap.pypa.io/get-pip.py
python get-pip.py
Once it is installed you can then install packages like this:
python -m pip install PACKAGE_NAME
(1) I have to install one python package (HTSeq) but i dont have root privileges.
The package need python 2.4 or latest version. We have python 2.3 on our cluster.
Thus I installed python 2.7 on my one local directory
using
./configure --prefix=/home/amit/tools/localpython
make
make install
(2) The package also requires numpy : so I also installed it on my local directory using:
/home/amit/tools/localpython/bin/python2.7 setup.py install --home=/home/amit/tools/localnumpy
and done
>>> sys.path.append("/home/amit/tools/localnumpy/lib/")
(3) I downloaded the tar file of HTSeq (Which i want to download) and run
/home/amit/tools/localpython/bin/python2.7 setup.py install --home=/home/amit/tools/localhtseq
it is throwing following error:
Could not import 'setuptools',
falling back to 'distutils'.
Setup script for HTSeq: Failed to import 'numpy'.
Please install numpy and then try again to install HTSeq.
Kindly provide me some hint on how to get over it
Thanks in advance
Setuptools is another requirement which you need to install that package.
One option is to use virtualenv to create a contained python environment. This can be made everywhere and is owned by the user who creates it.
To install virtualenv without admin rights (from this answer):
Download tar.gz of the latest version of virtualenv.
Unpack it.
You don’t even need to install it, just run virtualenv.py, for example:
wget http://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.7.1.2.tar.gz
tar -xzf virtualenv-1.7.1.2.tar.gz
/home/amit/tools/localpython/bin/python2.7 virtualenv-1.7.1.2/virtualenv.py env
env/bin/pip install HTSeq
env/bin/pip install numpy
Now run your script using the python binary in the virtual environment:
env/bin/python myscript.py
1) You have to install setuptools (it is necessary to run setup.py of your HTSeq).
Download sources tar.gz setuptools-0.6c11.tar.gz, unpack it, and then do the steps like you installed python2.7, but in the folder where you unpacked setuptools sources:
./configure --prefix=/home/amit/tools/localpython
make
make install
2) When you will install setuptools, a easy_install executable will apear in python2.7/scripts/ folder. You can use it to install packages easily:
/home/amit/tools/localpython/bin/python2.7/scripts/easy_install HTSeq
it will automatically find the package and will download and install it for you along with all dependencies.
Another way is to install pip as the local user and then install packages. As explained in the pip docs (check for OS specifics) you can install it as follows – obtain the get-pip.py script, then run it:
wget https://bootstrap.pypa.io/get-pip.py
python get-pip.py
Once it is installed you can then install packages like this:
python -m pip install PACKAGE_NAME