Installation
Cellsnp-lite depends on several external libraries such as htslib. We highly recommend installing cellsnp-lite via conda to avoid potential issues regarding dependency.
Install via conda (latest stable version)
conda install -c bioconda cellsnp-lite
Alternatively, you may also compile from source code.
Install from this Github Repo (latest stable/dev version)
Step 0: install dependencies
Cellsnp-lite mainly depends on zlib and HTSlib (v1.10.2+).
Note that HTSlib has some extra dependencies: liblzma, libbz2,
libcurl, and libcrypto.
The whole list of dependencies of building cellsnp-lite is:
gcc (have tested v4.8.5 on CentOS 7)
autoreconf
zlib
HTSlib >= 1.10.2
liblzma
libbz2
libcurl
libcrypto
All dependencies should have been installed into the system before installing cellsnp-lite.
If you already have a pre-installed HTSlib then go to next step.
Otherwise, a common way to install HTSlib is building from its Github repo
following this HTSlib instruction.
When HTSlib is successfully installed, there should be some executable files
(e.g., bgzip) and library files (e.g., libhts.a and libhts.so) in
htslib dir.
Step 1: compiling cellsnp-lite
Once all dependencies have been installed, it’s ready to compile cellsnp-lite,
git clone https://github.com/single-cell-genetics/cellsnp-lite.git
cd cellsnp-lite
autoreconf -iv
./configure # Needed for choosing optional functionality
make
make install # Optional, may need sudo privilege
By default, this will either build against a pre-installed HTSlib in
../htslib or build with a HTSlib in a system library path (e.g.,
/usr/lib).
You can alter this to a pre-installed HTSlib elsewhere by configuring with
--with-htslib=DIR.
The DIR should be either a dir containing a source tree with
libhts.a/libhts.so being in DIR, or a dir containing include
and lib subdirs with libhts.a/libhts.so being in DIR/lib.
Note that DIR must be absolute path and please use /home/<user>
instead of ~ if needed.