mdcao/npReader

Real-time conversion and analysis of Nanopore reads

I. Windows

1. Installation:
 - Download and install HDF-Java (https://www.hdfgroup.org/products/java/release/download.html) 

 - Download either japsa*.tar.gz or japsa*.zip and extract to a directory, e.g., c:\japsa

 - Set up the following environment variables:
    a. JSA_HOME to the directory where japsa was installed (e.g., c:\japsa)
    b. JHDF5_LIB to the library directory of HDF-Java that contains files jhdf5.dll and jhdf.dll, e.g., C:\Program Files\HDF_Group\HDFView\2.11.0\lib

2. Running
 Run jsa.np.f5readerGUI.bat from either command line or mouse click. On the GUI, enter the directory that the Metricho downloads to, and select output file.




II. Linux

1. Installation
 - Make sure libjhdf5 was installed
 - check out japsa 
$git clone https://github.com/mdcao/japsa

- Compile and install
$cd japsa
$make -f Makefile.main INSTALL_DIR=<INTALL_DIRECTORY> JLP=<PATH_TO_LIBJDH5.SO>

2. Run
$jsa.np.f5reader --folder <PATH_TO_DOWLOAD> -output <outputfile.fastq> -GUI