Building from source

Versions

This is an overview of the main versions of Lambda:

Repository	Branch	Description
https://github.com/seqan/lambda	lambda3	recommended branch
https://github.com/seqan/lambda	lambda2	previous master-branch (please upgrade)
https://github.com/seqan/lambda	lambda1	deprecated
https://github.com/h-2/seqan	feature/lambda	initially published; deprecated

Only lambda3 and lambda2 are supported and the instructions below will not work for older versions.

Getting the source

Check out the desired branch with git:

% git clone --recursive [-b BRANCHNAME] https://github.com/seqan/lambda.git

Alternatively, you can download a tarball from the releases page. Use a file that includes the submodules.

Build requirements

• operating systems: Linux, FreeBSD, macOS
• CPUs: x86_64 with SSE4 and POPCNT
• compilers: GCC ≥ 11 (no other compiler is supported!)
• cmake ≥ 3.10.0

Build instructions

% mkdir -p lambda-build/release
% cd lambda-build/release
% cmake ../../lambda
% make -j4

Please be aware that due to excessive use of templating and compile-time optimizations the build might take around 5min. macOS builds are slower and can take up to 15min.

If your most recent version of GCC is not the default, you have to specify the path. In many setups you then also need to adjust the paths to standard libraries, e.g.

% cmake ../../lambda \
-DCMAKE_CXX_COMPILER="/path/to/gcc_install/bin/g++" \
-DCMAKE_CXX_FLAGS="-L/path/to/gcc_install/lib64/" \
-DCMAKE_EXE_LINKER_FLAGS="-Wl,-rpath=/path/to/gcc_install/lib64/"

Build options (lambda3)

NAME	description	default
LAMBDA_STATIC_BUILD	Activate to include all libs in the binary. This will result in a bigger binary but in return work on different software than the one you are building from (e.g. compiler and OS version).	off
LAMBDA_WITH_BIFM	Activate codepaths for creating/reading bidirectional FM indexes.	off

Build options (lambda2)

NAME	description	default
LAMBDA_FASTBUILD	Setting this is useful for debugging, because the build will be faster. Only BLASTP and BLASTX support will be built.	off
LAMBDA_MMAPPED_DB	Use memory-mapped IO to access the database.	off
LAMBDA_LINGAPS_OPT	This activates optimized codepaths for linear gaps costs (i.e. additional gap open cost == 0). It has no drawbacks other than increased compile time and binary size.	off
LAMBDA_LONG_PROTEIN_SUBJ_SEQS	Make max protein sequence length == 4.3billion instead of 65,535. If you set this all previously built indexes will be incompatible!	off
LAMBDA_NATIVE_BUILD	Deactivating this will disable CPU-specific optimization, but in return your binary will work on different hardware than the one you are building from.	on
LAMBDA_STATIC_BUILD	Activate to include all libs in the binary. This will result in a bigger binary but in return work on different software than the one you are building from (e.g. compiler and OS version).	off

To build portable binaries of Lambda, deactivate native builds and activate static builds, i.e. pass -DLAMBDA_NATIVE_BUILD=0 -DLAMBDA_STATIC_BUILD=1 to cmake.

Please note that it is not possible to build completely static binaries on Mac OS X, but the flag at least packages the compiler specific bits into the binary.