I am trying to deploy a gene annotation pipeline for eukaryote genomes recently. The genewise (or “Wise2”) package (http://www.ebi.ac.uk/~birney/wise2/) is one of many packages that I need for this purpose. The version that I am trying to install here is the latest one (v2.4.1), which can be obtained following this link: http://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz . From the installation instruction, it seemed all I need to do is simply typing “make all” in the “./src” directory but in reality there are a few more steps needed before I get it compiled successfully. So I am recording these steps here for my future reference and hope it can help anyone who encountered the same problem.

#!/usr/bin/sh

# install glib2-devel package if it has not been installed on the system
<span class="im">sudo yum install -y glib2-devel</span>

# download and decompress the package
wget <a title="http://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz" href="http://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz" target="_blank">http://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz</a>
tar xvzf wise2.4.1.tar.gz

# make some necessary changes in the makefile and source files.
cd wise2.4.1/src
# Here we need to modify makefile to replace "CC = cc" with "CC = gcc" in Line 25 and save the change
find ./ -name makefile |xargs sed -i 's/glib-config/pkg-config --libs glib-2.0/'
cd ./HMMer2/
sed 's/getline/getline_new/' sqio.c  > a &&  mv a sqio.c
cd ../models/
# Change phasemodel.c to replace "if( !isnumber(line[0]) ) {" with "if( !isdigit(line[0]) ) {" in Line 23
cd ..
make all

Now genewise should be correctly compiled and you can find in the “wise2.4.1/src/bin” directory.

References
https://www.biostars.org/p/87823/