Installing Taffy CLI/C Library

Do build this repo clone the repo as follows and then make:

git clone https://github.com/ComparativeGenomicsToolkit/taffy.git --recursive
cd taffy && make

To test the installation do:

make test

This will run the unit tests. You should see that all tests pass okay. You will then want to add the taf/bin directory to your path.

htslib dependency

Taffy uses htslib (via pkg-config --exists htslib at build time) for bgzip support and HTTP/S3 input. If pkg-config doesn't find an htslib install, the build still succeeds but bgzipped input and URL input are disabled.

You can also point at a non-pkg-config htslib install by setting HTSLIB_CFLAGS and HTSLIB_LIBS in the environment before make.

URL/HTTPS/S3 input requires htslib with libcurl

taffy view -r SEQ:s-e -i https://... (or s3://..., etc.) routes through htslib's libcurl-backed hFILE layer. Most distro/conda htslib packages have this enabled. If you built htslib from source, you may need to rerun configure with libcurl support:

cd htslib
autoreconf -i           # only if there's no ./configure yet
./configure --enable-libcurl
make

If your htslib lacks libcurl, taffy will print a clear error suggesting the above when a URL input is given.