Download LDAK

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LDAK-KVIK is included in LDAK, a command-line software, that can be run on either Linux or a Mac. We strongly recommend the Linux version, as it will often be much faster than the Mac version. Note that LDAK does not run on Windows, so we suggest using a Linux server (for example, you can use putty to ssh into your local computer cluster).

There are four ways to obtain LDAK: you can install LDAK via a command line, you can manually download the LDAK executable, you can install LDAK via conda, or you can compile your own version of LDAK from the source code.

Please note that LDAK-KVIK is currently only released on the Linux version of LDAK, the MAC version will soon be released.

1. Download via command line

For Linux, open a terminal window (go to Applications / System Tools / Terminal), then install the Linux executable of LDAK using the command line:

wget https://github.com/dougspeed/LDAK/raw/refs/heads/main/ldak6.1.linux

For MAC, open a terminal window (go to Finder / Applications / Utilities), then install the Mac executable of LDAK using the command line:

wget https://github.com/dougspeed/LDAK/raw/main/ldak6.mac

Note that it might be necessary to grant permission to run the file using chmod a+x ldak6.linux (for Linux) or chmod a+x ldak6.mac (for Mac).

2a. Download the Linux executable

  • Download the Linux executable file from GitHub (https://github.com/dougspeed/LDAK/blob/main/ldak6.1.linux). The file can be downloaded using the hotkey ctrl+shift+s, or by selecting ‘download’ in the three-dotted box.

  • Open a terminal window (on my Linux, I go to Applications / System Tools / Terminal)
  • Type the name of the file (for example, /home/doug/Downloads/ldak6.linux), or if you are in the same folder as the executable file, you can simply type ./ldak6.linux. If compatible with your system, this should produce the LDAK welcome screen.

Note that if your computer tells you that you do not have permission to run the file, then first run chmod a+x ldak6.linux

2b. Download the MAC executable

  • Download the Linux executable file from GitHub (https://github.com/dougspeed/LDAK/blob/main/ldak6.mac). The file can be downloaded using the hotkey ctrl+shift+s, or by selecting ‘download’ in the three-dotted box.

  • Open a terminal window (go to Finder / Applications / Utilities)
  • Type the name of the file (for example, Downloads/ldak6.mac), or if you are in the same folder as the executable file, you can simply type ./ldak6.mac. If compatible with your system, this should produce the LDAK welcome screen.

Note that if your computer tells you that you do not have permission to run the file, then first run chmod a+x ldak6.mac

3. Install LDAK via conda (Linux systems only)

LDAK can be installed via conda as follows:

# create a new environment and install LDAK
conda create -n ldak_env -c genomedk ldak6

# load the new environment 
conda activate ldak_env

# check LDAK starts
ldak6

The final command should display an overview of the LDAK commands. Note that all our examples use ldak6.linux to run LDAK-KVIK, which should be replaced by ldak6 if downloaded via conda.

4a. Compile LDAK from source code (Linux)

The pre-compiled Linux version uses the Intel MKL Libraries. We use the command:

gcc --static -O3 -o ldak6.linux ldak/ldak.c ldak/libqsopt.linux.a -m64 -Wl,--start-group ${MKLROOT}/lib/libmkl_intel_lp64.a ${MKLROOT}/lib/libmkl_gnu_thread.a ${MKLROOT}/lib/libmkl_core.a -Wl,--end-group -lgomp -lpthread -lm -ldl -lz -I${MKLROOT}/include -fopenmp -L/home/doug/opt/lib -I/home/doug/opt/include

Should you wish to compile a Linux version yourself, please download and unzip the source code (https://github.com/dougspeed/LDAK), then from inside that folder run a command similar to

gcc -O3 -o ldak6 ldak.c libqsopt.linux.a -lblas -llapack -lm -lz -fopenmp
chmod a+x ldak6

The exact command will depend on which libraries you have installed. This should take less than a minute to complete. Note that if you do not have Intel MKL Libraries installed, you will be required to turn off the MKL libraries, by editing Line 63 of ldak.c (replace #define MKL 1 with #define MKL 0). If you are required to do this, then your self-compiled version will likely be slower than the pre-compiled version.

4b. Compile LDAK from source code (Mac)

Should you wish to compile a Linux version yourself, please download and unzip the source code (https://github.com/dougspeed/LDAK), then from inside that folder run a command similar to

gcc -O3 -o ldak6.mac ldak.c libqsopt.mac.a -lblas -llapack -lm -lz
chmod a+x ldak6.mac

The exact command will depend on your system and which libraries you have installed. This should take about a minute to complete. Note that you will be required to turn off the MKL libraries, by replacing #define MKL 1 with #define MKL 0 (this code is located at approximate Line 54 in the file ldak.c). Further, it may be necessary to add -arch x86_64 to the above command, and/or to install xcode, by first running the command

xcode-select --install