Install
HiCOPS uses a standard CMake installation. Set the environment variables CC and CXX before executing CMake to specify the compilers. By default, HiCOPS enables OpenMP and MPI and disables instrumentation support. HiCOPS will search the CMAKE_PREFIX_PATH for Timemory installation.
Environment
- GCC 7.2+ compiler with C++14, OpenMP and threading
- MPI
- Python 3.7+
- CMake 3.11+
- Linux based OS such as Ubuntu 16.04+, CentOS7+.
Important: Please make sure that your MPI distribution supports multiple threads (MPI thread multiple) option.
Required Packages
Install all required packages by following the instructions here.
Instrumentation Support
Optional: Install Timemory to enable instrumentation by following the instructions here.
Install HiCOPS
Install HiCOPS using Git & CMake using the following steps:
# clone
$ git clone https://github.com/mhaseeb123/hicops
$ cd hicops
$ mkdir build && cd build
# configure with CMake
$ CC=$(which gcc) CXX=$(which g++) cmake .. [CMAKE_OPTIONS] -G [BUILD_SYSTEM] [HICOPS_OPTIONS]
# build and install
$ make install -j [JOBS]
# append hicops-core lib path to LD_LIBRARY_PATH.
$ export LD_LIBRARY_PATH=$PWD/../install/lib:$LD_LIBRARY_PATH
Note: Compiling HiCOPS with Timemory enabled may take some time (~ 3-5 minutes)
CMake Options
The available CMake options for HiCOPS include:
| Option | Description |
|---|---|
USE_MPI |
Enable MPI support. Set to: ON (default), OFF |
USE_TIMEMORY |
Enable timemory interface. Set to: ON, OFF (default) => Requires timemory installation. |
USE_MPIP_LIBRARY |
Enables the MPIP data_tracker via Timemory. Set to: ON, OFF (default) => Requires timemory installation |
TAILFIT |
Use the tailfit method instead of Gumbelfit for e-value computation. Set to: ON (default), OFF |
PROGRESS |
Display HiCOPS progress marks. Set to: ON (default), OFF |
MAX_SEQ_LEN |
Allowed maximum peptide sequence length. Set to: 7 to 60. Default: 60 |
QALEN |
Maximum number of top K peaks to keep when spectrum preprocess. Default: 100 |
QCHUNK |
Max size of each batch extracted from the dataset. Default: 10000 |
MAX_HYPERSCORE |
Maximum allowed hyperscore computed. Default: 100 |
Available CMake build control options include:
| Option | Description |
|---|---|
CMAKE_INSTALL_PREFIX |
Set the installation path for HiCOPS, must be a writable directory without sudo |
CMAKE_BUILD_TYPE |
Build type. Set to: Release, Debug, MinSizeRel, RelWithDebInfo (default) |
CMAKE_CXX_STANDARD |
C++ standard. Set to: 14 (default), 17 |