gridsstools Makefile does not autodetect if libdeflate is available

[astulaaa]

I followed github instalation guide:

git clone http://github.com/PapenfussLab/gridss/
cd gridss
git submodule init
git submodule update
cd src/main/c/gridsstools/htslib/
autoheader
autoconf
./configure && make
cd ..
autoheader
autoconf
./configure && make all

and got this error at the last step:

/usr/bin/ld: cannot find -ldeflate
collect2: error: ld returned 1 exit status
Makefile:25: recipe for target 'gridsstools' failed
make: *** [gridsstools] Error 1

What happened and how can I fix it?

Thank you,
Asta

[d-cameron]

Your options are:

• Install libdeflate on your system
• Edit the src/main/c/gridsstools/Makefile and remove -ldeflate
• Use conda to install gridss
• Run gridss from the gridss/gridss:latest docker image
• Use the pre-compiled binary from the github releases page