From 7b767c7940476100038a31b1d9d9924eaa385572 Mon Sep 17 00:00:00 2001 From: Minh Duc Cao Date: Wed, 5 Aug 2015 12:45:35 +1000 Subject: [PATCH] included in Japsa --- README | 42 +++--------------------------------------- 1 file changed, 3 insertions(+), 39 deletions(-) diff --git a/README b/README index 1879d0b..269e01a 100644 --- a/README +++ b/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 -$make -f Makefile.main INSTALL_DIR= JLP= - -2. Run -$jsa.np.f5reader --folder -output -GUI - - - You can even pass the fastq to a downstream analysis program, such as bwa: - - $jsa.np.f5reader --folder -output - -GUI | tee output.fastq | bwa mem - > output.sam - - -