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INSTALL.md

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Important Notes

  • Only CentOS 6 and Ubuntu 12.10 and up have been tested.
  • Only a Linux 64-bit version of our software is available at this time.
  • Currently, the default install path is valid only on UNIX-like platforms.
  • Version 1.10 and later has switched to using SQLite for database management.

Requirements

Hardware

VNTRseek was designed around multiprocessing on a large computer. Minimum specs suggested are 8 cores, 32GB of RAM, and 1TB of file space. This will run a sample of 700M human FASTA reads in roughly 30 hours.

Software

Latest versions preferred.

  • GCC (>= 4.1.2)
  • Perl (>= 5.24.0)
    • DBI and DBD::SQLite modules
  • SQLite (>= 3.37.0)
  • TRF (>= 4.09)
  • samtools (>= 1.8)
  • GLIBC (>= 2.14)
  • CMake (>= 3.2)

TRF is downloaded during installation. If the download fails, you can download it manually from github and save it as trf409-ngs.linux.exe in the build directory (see Installation below).

Installation

To build and install to the default directory, download the VNTRseek-N.N.N.tar.gz file from the latest release and run the following commands:

tar xzvf VNTRseek-N.N.N.tar.gz
cd VNTRseek-N.N.N
mkdir build
cd build
cmake ..
make install # or sudo make install, if needed

By default, this will install the pipeline to /usr/local/vntrseekN.N.N (e.g., /usr/local/vntrseek2.0.3) and create a symbolic link at /usr/local/bin/vntrseek that points to the main program at /usr/local/vntrseekN.N.N/vntrseek.pl.

If you would like to choose a different installation prefix, add the -DCMAKE_INSTALL_PREFIX option to the cmake call, e.g.:

# use this for an absolute path to vntrseekN.N.N
cmake -DCMAKE_INSTALL_PREFIX=<absolute_prefix> ..

# use this to create a subdirectory under your home directory for vntrseekN.N.N
cmake -DCMAKE_INSTALL_PREFIX=${HOME} ..

If you install to a non-standard location, you may need to add the /bin with the link (e.g., <absolute_prefix>/bin or ${HOME}/bin) to your PATH variable.

You can change your default compiler using the -DCMAKE_C_COMPILER option. For example, to use clang:

cmake -DCMAKE_C_COMPILER=clang ..

If you installed this pipeline as root, and are creating an INDIST file you may need to run it as root unless you give your user permission to write to the installation directory.

Uninstalling

On UNIX, run:

xargs rm < install_manifest.txt # or sudo xargs rm < install_manifest.txt

from the build directory you created above. The directory will remain, however, so you will not lose any reference files.