Difference between revisions of "SMRT Analysis: Viewing HTML reports on Abel"
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== -on the local machine (PC) == | == -on the local machine (PC) == | ||
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*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/]) | ||
| − | * | + | *Use the default installation options, including the "Normal PuTTY link SSH client". Not including PuTTY may cause problems, even if you have PuTTY installed previously. |
| − | == -on Abel | + | == -on Abel == |
Download the QtWeb web browser into a local folder, unzip and give permissions: | Download the QtWeb web browser into a local folder, unzip and give permissions: | ||
| − | + | <div style="line-height:90%; background-color: LightGray; border-style: solid; border-width:1px; font-family:courier new,courier,monospace;"> | |
mkdir qtWeb | mkdir qtWeb | ||
| Line 23: | Line 22: | ||
wget [http://www.qtweb.net/downloads/QtWeb-elf386.zip http://www.qtweb.net/downloads/QtWeb-elf386.zip] | wget [http://www.qtweb.net/downloads/QtWeb-elf386.zip http://www.qtweb.net/downloads/QtWeb-elf386.zip] | ||
| − | unzip QtWeb-elf386.zip | + | unzip QtWeb-elf386.zip |
| + | chmod 777 QtWeb | ||
| + | </div> | ||
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*select "Using PuTTY (plink.exe)" | *select "Using PuTTY (plink.exe)" | ||
**enter the "Connect to computer" ("abel.uio.no"), "username" and "password" values. | **enter the "Connect to computer" ("abel.uio.no"), "username" and "password" values. | ||
| + | ***If you have a "long" password (>14 characters), it will not fit into the password textbox. In this case, leave the password empty. When connection, copy the password from a text editor (such as Notepad) into the password dialog box (typing the password may crash the program). | ||
**Click "Next" | **Click "Next" | ||
| − | |||
*Click "Next" | *Click "Next" | ||
*Click "Finish" | *Click "Finish" | ||
You will now see the Xming terminal window. Go to the QtWeb folder and lanch the browser: | You will now see the Xming terminal window. Go to the QtWeb folder and lanch the browser: | ||
| − | + | <div style="line-height:90%; background-color: LightGray; border-style: solid; border-width:1px; font-family:courier new,courier,monospace;"> | |
cd qtWeb | cd qtWeb | ||
./QtWeb | ./QtWeb | ||
| − | + | </div> | |
In the browser address bar, enter the full filename of the index.html file ("/path/to/outputFolder/index.html") and press enter. | In the browser address bar, enter the full filename of the index.html file ("/path/to/outputFolder/index.html") and press enter. | ||
Latest revision as of 15:38, 24 March 2015
Contents
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)
- Download and install the Xming X11 client (see http://sourceforge.net/projects/xming/)
- Use the default installation options, including the "Normal PuTTY link SSH client". Not including PuTTY may cause problems, even if you have PuTTY installed previously.
-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.
- If you have a "long" password (>14 characters), it will not fit into the password textbox. In this case, leave the password empty. When connection, copy the password from a text editor (such as Notepad) into the password dialog box (typing the password may crash the program).
- Click "Next"
- enter the "Connect to computer" ("abel.uio.no"), "username" and "password" values.
- 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.
