Difference between revisions of "SMRT Analysis: Viewing HTML reports on Abel"

From mn/ibv/bioinfwiki
Jump to: navigation, search
Line 11: Line 11:
 
*Download and install the PuTTY SSH client (see [http://ssh.uio.no/index-eng.html http://ssh.uio.no/index-eng.html])
 
*Download and install the PuTTY SSH client (see [http://ssh.uio.no/index-eng.html http://ssh.uio.no/index-eng.html])
 
*Download and install the Xming X11 client (see [http://sourceforge.net/projects/xming/ http://sourceforge.net/projects/xming/])
 
*Download and install the Xming X11 client (see [http://sourceforge.net/projects/xming/ http://sourceforge.net/projects/xming/])
*Download the plink.exe file (see [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html]).
+
*Download the <span style="font-family:courier new,courier,monospace;">plink.exe</span> file (see [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html]).
  
 
== -on Abel: ==
 
== -on Abel: ==
Line 38: Line 38:
 
**enter the "Connect to computer" ("abel.uio.no"), "username" and "password" values.
 
**enter the "Connect to computer" ("abel.uio.no"), "username" and "password" values.
 
**Click "Next"
 
**Click "Next"
*Select the downloaded plink.exe file
+
*Select the downloaded <span style="font-family:courier new,courier,monospace;">plink.exe</span> file
 
*Click "Next"
 
*Click "Next"
 
*Click "Finish"
 
*Click "Finish"

Revision as of 14:25, 13 March 2015

Introduction

In addition to the output data files, the smrtpipe program creates output reports for most protocols. These reports contain statistics and figures describing the quality of the results. To open such a report, the outputFolder/index.html file must be opened in a web browser.

It is possible to do this by downloading the entire outputFolder from Abel to a local machine. But often the outputFolder will contain so much data to make this problematic. Instead, it is possible to directly open the index.html file on Abel, display the results in a web browser on your local machine. This involves opening a web browser on Abel, and using the X windows system to view the graphical user interface on the local machine. The following steps will acomplish this using a Win7 PC as the local machine.

Installation of the required programs

-on the local machine (PC)

-on Abel:

Download the QtWeb web browser into a local folder, unzip and give permissions:

mkdir qtWeb

cd qtWeb

wget http://www.qtweb.net/downloads/QtWeb-elf386.zip

unzip QtWeb-elf386.zip

chmod 777 QtWeb


Opening the report in the browser

On your local machine, after launching Xming:

  • select "multiple windoes", click "Next"
  • select "Start a program", click "Next"
  • select "Using PuTTY (plink.exe)"
    • enter the "Connect to computer" ("abel.uio.no"), "username" and "password" values.
    • Click "Next"
  • Select the downloaded plink.exe file
  • Click "Next"
  • Click "Finish"

You will now see the Xming terminal window. Go to the QtWeb folder and lanch the browser:

cd qtWeb

./QtWeb

In the browser address bar, enter the full filename of the index.html file ("/path/to/outputFolder/index.html") and press enter.

Hint: you can get hold of the index.html filename (without typoes) by opening another Abel terminal window using PuTTY, and typing

more /path/to/index.html

using TAB to autocomplete the folder names. Copy the filename (but not the "more" statement) to the QtWeb address bar.