Skip to content

Latest commit

 

History

History
89 lines (61 loc) · 2.44 KB

INSTALL.md

File metadata and controls

89 lines (61 loc) · 2.44 KB
Raw

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.

  • samtools
  • Perl (>= 5.24.0)
    • DBI and DBD::SQLite modules
  • SQLite (>= 3.37.0)

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

Building requires cmake (http://www.cmake.org/), minimum version 3.0

Additionally you will need GCC version 4.1.2 on Mac/Linux/CYGWIN or a compatible compiler.

Installation

To build and install to the default directory, run the following commands:

tar xzvf vntrseekN.NN.tar.gz
cd vntrseekN.NNsrc
mkdir build
cd build
cmake ..
make install # or sudo make install, if needed

By default, this will install the pipeline to /usr/local/vntrseekN.NN (eg, /usr/local/vntrseek2.0.0).

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

cmake -DCMAKE_INSTALL_PREFIX=<absolute_prefix> ..

# install to home at ${HOME}/vntrseekN.NN
cmake -DCMAKE_INSTALL_PREFIX=${HOME} ..

If you install to a non-standard location, you may need to add <absolute_prefix>/bin to your PATH variable (e.g., if your prefix was /opt, you will need to have /opt/bin in your PATH).

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.