included in Japsa

README

@@ -1,40 +1,4 @@
-Real-time conversion and analysis of Nanopore reads
+npReader is a tool for real-time conversion and analysis of Nanopore 
+reads. It is included in the Japsa package, and its documentation is 
+on http://japsa.readthedocs.org/en/latest/tools/jsa.np.f5reader.html
 
-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:\JapsaHome. (So you will see c:\JapsaHome\lib\japsa\japsa.jar)
-
- - Set up the following environment variables:
-    a. JSA_HOME to the directory where japsa was installed (e.g., c:\JapsaHome)
-    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
-
- 
- You can even pass the fastq to a downstream analysis program, such as bwa:
-
- $jsa.np.f5reader --folder <PATH_TO_DOWLOAD> -output - -GUI | tee output.fastq | bwa mem <path_to_index> - > output.sam
-
- 
-