How to install Discovar in Ubuntu 20.04?

Problem:

You compiled Discovar DE NOVO using make all, you get this error:

make: *** [Makefile:288: install-recursive] Error 1

Solution:

Compile using gcc 4.x version.

Step by step:

Install requirements:

$ sudo apt-get install libjemalloc-dev
$ sudo apt-get install zlib1g-dev
$ sudo apt install build-essential

Install samtools (required if using bam files)
```
$ sudo apt-get install samtools
```
Add a repository. Open the file:
```
$ sudo gedit /etc/apt/sources.list
```

Add these lines, preferably at the end of the file.

#RPA ADDED
deb http://us.archive.ubuntu.com/ubuntu bionic main universe

Install gcc and g++ 4.8 version. Open a Terminal and execute:
```
$ sudo apt upgrade && apt install gcc-4.8 g++-4.8
```

Configure multiple gcc versions.

$ sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 40 \
--slave /usr/bin/g++ g++ /usr/bin/g++-4.8
$ sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 90 \
--slave /usr/bin/g++ g++ /usr/bin/g++-9 

Choose gcc-4.8 version. Type in Terminal:

$ sudo update-alternatives --config gcc

Install the libieee library.

$ sudo ln -sv /usr/lib/x86_64-linux-gnu/libieee1284.so.3.2.2 \
/usr/lib/x86_64-linux-gnu/libieee.so
$ sudo ln -sv /usr/lib/x86_64-linux-gnu/libieee1284.so.3.2.2 \
/usr/lib/x86_64-linux-gnu/libieee1284.so.3
$ sudo ldconfig

Install Discovar. Open the INSTALLfile and follow the instructions. A short way:
```
$ tar xzf discovardenovo-NNNNN.tar.gz
$ cd discovardenovo-52488/
$ ./configure
$ make all
$ make install
```
where NNNNN is the Discovar version, in this example 52488 is the version.
Delete the repository url. Open the file and delete the last two lines added previously.
```
$ sudo gedit /etc/apt/sources.list
```
This step is neccesary for stopping using a previous Ubuntu repository version.

Source:

I solved this problem based in Discovar forum user group:

https://groups.google.com/a/broadinstitute.org/g/discovar-user-forum

searching this: Makefile:288 install-recursive

https://groups.google.com/u/1/a/broadinstitute.org/g/discovar-user-forum/c/RWFyF11-cjc/m/VLwHBQqeCAAJ

Install gcc in Ubuntu 20.04

https://linuxize.com/post/how-to-install-gcc-on-ubuntu-20-04/

Discovar - manual and faq

https://software.broadinstitute.org/software/discovar/blog/?page_id=19

How to compile with gcc

https://stackoverflow.com/questions/27390078/gcc-compiling-c-code-undefined-reference-to-operator-newunsigned-long-lon/27390293

Linux: C/C++ Libraries

http://chenweixiang.github.io/2015/12/18/linux-series-05-libraries.html

Discovar de novo manual

https://banana-slug.soe.ucsc.edu/contributors:team_5:discovar_de_novo_manual