/npReader

Permalink
npReader/README.md
Newer
Older
Raw Normal view History
100644 58 lines (32 sloc) 2.37 KB
Feb 26, 2016 @mdcao Create REAME.md
1 ### Introduction
2
3 npReader is a tool to facilitate real-time conversion and analysis of Nanopore sequencing
Feb 26, 2016 @mdcao Update README.md
4 data. It was developed as part of [Japsa](https://github.com/mdcao/japsa) package where its source code and documentation reside.
Feb 26, 2016 @mdcao Create REAME.md
5
6 ### Quick installation guide
7
8 ######Under Linux/Mac
9
10 1.Install JHI5 using the packaging tool of your operating system distribution. For example, under Debian/Ubuntu
11
12 sudo apt-get install libjhdf5-jni
13
Feb 9, 2017 @mdcao Update README.md
14 For MacOS, you can download and install hdfviewer from https://support.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdf-java-2.10.1/bin/
Feb 9, 2017 @mdcao Update README.md
15
Feb 26, 2016 @mdcao Create REAME.md
16 2.Obtain the source code, compile and install
17
18 git clone https://github.com/mdcao/japsa
19 cd japsa
20 make install JLP=/usr/lib/jni \
21 [INSTALL_DIR=~/.usr/local \]
22 [MXMEM=7000m \]
23 [SERVER=true \]
24
Feb 9, 2017 @mdcao Update README.md
25 Change the JLP directive to point to where JHI5 is installed if needed. In a standard installation, the directive would be /usr/lib/jni for Linux or /Applications/HDFView.app/Content/Resources/lib for MacOS.
Feb 26, 2016 @mdcao Create REAME.md
26
27 3.Set the environment variable PATH to include the installation directory, eg,
28
29 set PATH=~/.usr/local/bin:$PATH
30
31 4.Usage information
32
Sep 26, 2016 @mdcao change name
33 jsa.np.npreader --help
Feb 26, 2016 @mdcao Create REAME.md
34
35 ######On any OSs
36
Feb 9, 2017 @mdcao Update README.md
37 1.Install hdf from https://support.hdfgroup.org/downloads/. The current version (1.7-02a) was tested with hdf version 2.10.1, which can be downloaded from https://support.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdf-java-2.10.1/bin/. During installation of hdf, please take note of where the library is installed.
Feb 26, 2016 @mdcao Create REAME.md
38
39 2.Download pre-compiled Japsa of the latest release from https://github.com/mdcao/japsa/releases
40
Feb 9, 2017 @mdcao Update README.md
41 3.Unzip the package, and run install.sh (for Linux/Mac) or install.bat (for Windows) and follow the prompt. Enter the path to hdf library when asked.
Feb 26, 2016 @mdcao Create REAME.md
42
43
44 ### Documentation
45
46 Detailed usage of npReader including setting up streaming analysis of nanopore sequencing in
Sep 26, 2016 @mdcao change name
47 genuine real-time can be found from http://japsa.readthedocs.org/en/latest/tools/jsa.np.npreader.html
Feb 26, 2016 @mdcao Update README.md
48
49 General information of Japsa can be found on its [ReadTheDoc](http://japsa.readthedocs.org/en/latest/)
Feb 26, 2016 @mdcao Update README.md
50
51 ### Reference
52
53 If you find npReader useful for your research, please cite its publication:
54
55 Cao MD, Ganesamoorthy D, Cooper MA, Coin LJM, (2016). Realtime analysis and visualization of MinION sequencing data
Feb 26, 2016 @mdcao Update README.md
56 with npReader. Bioinformatics, 32(5):764–766. DOI:[10.1093/bioinformatics/btv658](http://dx.doi.org/10.1093/bioinformatics/btv658)
Feb 26, 2016 @mdcao Update README.md
57