I need some help to install the ABySS assembler on PuTTY (virtual Linux) without root permission (as it takes a long time going via IT department etc.). To be honest I’ve no idea where to start from, so I’ll be very appreciated for step-by-step guide if that is not too much to ask. Thanks in advance.
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Answer
If you are referring to the software here, then it should be sufficient to follow the instructions here. Specifically, you should take note of the part labelled To install ABySS in a specified directory:, and specify a directory in your home directory that you have write access to. For example, I might:
mkdir ~/abyss ./configure --prefix=$HOME/abyss make make install
Note that I have removed sudo from before make install, so that you are trying to run the installation as a user rather than root. make install will put the software wherever you specified with --prefix.
However, this all depends upon the source code for any libraries upon which ABySS depends existing on your system as well. I expect you will fail at the ./configure step because some library is missing. In this case download the source code for those libraries and tell configure where you have put them (in your home directory), following the example given for Boost on that same page.