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Nabil-Fareed Alikhan

Getting tRNAscan to work on Linux

tips1 min read

A friend/collaborator was having problems getting tRNAscan-SE to work on his Debian machine (I think it was Debian). We came up with a fix for it that I'd like to share.

tRNAScan-SE predicts transfer RNA genes in a nucleotide sequence. It was written by Todd Lowe & Sean Eddy (The paper) and it's very, very good at what it does but there is a glitch with compiling it on my Fedora 14 installation & my buddy's Debian machine. This is what happens when we try to compile it:

So, apparently on some linux distros, 'getline' function is an environment variable and creates a conflict during tRNAscan-SE installation. (This is basically what's written in the compile error).

BUT to fix this problem, run this command in the tRNAscan-SE directory:

This command will change all getline variables on the file sqio.c to getline2, avoiding conflicts.

Problem solved!