Helsinki 19 Jan Practical course in genome bioinformatics DAY 0

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1 Helsinki 19 Jan Practical course in genome bioinformatics DAY 0 This document can be downloaded at: The upcoming course homepage will be located at: 1. Connecting to CSC-server Taito (taito-shell.csc.fi) using PuTTY PuTTY is a secure shell (ssh) client application can be found in the Start menu (button with the Windows icon on the bottom left side of the screen). Go to All Programs > PuTTY > PuTTY. In the opening window, type the following information: Host Name (or IP address): taito-shell.csc.fi Then click Open. When connecting for the first time a PuTTY Security Alert is shown. This is a completely normal notification when connecting to a new host. Click Yes. The server will now ask your login credentials. Those are the ones on the piece of paper that was given to you. If you already have your own CSC credentials, you can use those. Otherwise, enter the following information: login as: (your username from the paper) Press Enter. lhbioxx@taito-shell.csc.fi's password: (your password from the paper) Press Enter. Typos are quite frequent when entering credentials. If login fails, just re-open PuTTY and repeat the previous steps. With successful login, a welcoming message from the server is shown on the PuTTY screen and finally, a command line with the characteristic green cursor: [lhbioxx@c3xx ~]$ The X:s in the above example are numbers and they do differ between users. This is due to the unique user names and various login nodes in use. Please always log in with the same exact username that was given to you on the paper! 2. Connecting to CSC-server taito using WinSCP

2 WinSCP will provide a graphical user interface into the taito.csc.fi file system. This is the most convenient way in Windows of managing files between your local computer and the server. WinSCP can be found in the start menu (button with the Windows icon on the bottom left side of the screen). Go to All Programs > WinSCP In the opening window, fill in the following information: Host name: taito-shell.csc.fi User name: (your username from the paper) Password: (your password from the paper) Then click the Login button on the bottom of the window. Again, a Warning is shown when connecting for the first time. This is a completely normal notification when connecting to a new host. Click Yes. 3. Learning UNIX basics Go back to PuTTY. If the connection is not open already, connect to taito-shell.csc.fi using PuTTY as in chapter 1 of these exercises. Now you should see a command line with something like this: [lhbioxx@c30x ~]$ UNIX is a family of operating systems and Linux is called a Unix-like operating system because of the command line resembling original UNIX and mainly following the same commands and protocols. The commands we use in these exercises apply to all UNIX and Unix-like operating systems. 3.1 Where are we? Type the following command and press Enter: pwd pwd is short for present working directory and this is just what this command will display. The default login directory is called a home directory.

3 It is also useful to see what is inside a directory. You can do this by typing: ls -all 3.2 Hello world! It is customary to greet the world somehow in a new computing environment. On UNIX command line you can do this by typing the following: echo Hello world! The echo command will print out useful information in the command line. Next, please type: echo $WRKDIR This will show you the location of your CSC working directory that has much more space than the home directory. This location info is useful when you navigate into the working directory using WinSCP. Change now into the working directory by typing command: You can then confirm this change by typing: pwd 3.3 Using a text editor for files Change into the working directory if you are not there already by typing command: Open a new text file called test.txt by typing: nano test.txt This opens a new editable area for text in a popular UNIX editor called nano. Write something

4 e.g. Hello world! to the area. To save the file, press Ctrl and O-key simultaneously (Ctrl-O). Then press Enter. Finally, press Ctrl and X-key simultaneously (Ctrl-X) to exit the editor. If you now type ls -all you will see your file listed in the directory. You can quickly view the contents of the file by typing: cat test.txt 3.4 Creating a new directory and copying files Change into the working directory if you are not there already by typing command: Create a new directory by typing: mkdir preview If you now type ls -all you will see your new directory listed in the directory. Change into the new directory by typing: cd preview If you now type ls -all you will see that the directory is empty. You can change back to the working directory ( parent directory ) by typing: cd.. Now copy the test.txt file into the preview directory by typing: cp test.txt preview By changing into the preview directory (cd preview) and typing ls -all you can now see a copy of test.txt listed in the directory. To confirm that the copy is proper, check the contents of the file by typing: cat test.txt 4. Loading the biokit module for analysis If the connection is not open already, connect to taito-shell.csc.fi using PuTTY as in

5 chapter 1 of these exercises. Navigate to your working directory if not there already (cd $WRKDIR) CSC serves all national scientific computing for multiple fields of sciece. They have bundled the field-specific applications into suitable modules in their Linux environment. The bioinformatics module is called biokit. You can load the module by typing: module load biokit This will quickly load and list all programs and their versions in the module. With these steps complete, you are ready to all practical work on the course. 5. Running a bioinformatics program Load the biokit module if you haven't already: module load biokit Navigate into your working directory (). Then create 2 new directories: mkdir bioinfo2017 mkdir bioinfo2017/day0 The day0 directory was hereby created within the bioinfo2017 directory. Then navigate into the day0 directory: cd bioinfo2017/day0 Next, get some material, namely a test FASTQ file for some bioinformatics analysis: rsync /wrk/lhbio1/bioinfo2016/day0/anabaenasyke758a_paired_r1.fastq./ The dot and slash at the end of the line are very important to include. You will see that a file called AnabaenaSYKE758A_paired_R1.fastq has appeared in your day0 directory. View the contents of the file by typing: less AnabaenaSYKE758A_paired_R1.fastq TIP: Tapping the TAB-key while inputing a filename will automatically fill the correct filename for you. Same goes for directory paths when using other commands. You can scroll around the file with the up and down arrow keys. The less command is exited by pressing the q key. Next, we will check quality of the reads in the FASTQ file: fastqc AnabaenaSYKE758A_paired_R1.fastq

6 Running the program creates an HTML file (a web page) and a.zip file. Copy the HTML file into your local computer (using WinSCP) and open it with an internet browser (Internet Explorer or Firefox). You have just completed a quality control for a sequencing reads FASTQ file, congratulations! 6. Running programs with a graphical user interface in Taito Tomorrow we will run a software called Mauve that we will use to view multiple sequence alignments. We will now test that everybody can get Mauve working. As the PuTTY program by default provides only a command-line access to taito-shell.csc.fi, we will need to make a change to the connection settings in order to be able to run GUI programs there. This is called X11-windowing. For this step, you will need to shut down your existing PuTTY connection to taito-shell.csc.fi. A controlled exit is possible with the exit command: exit On the the other hand the X in the top right corner will terminate the connection but will also terminate the whole PuTTY program on the same. Both ways work, but the first approach will leave PuTTY configuration open for another connection. Start the X-window server in Windows. This can be located from Start menu > All programs > Xming (OR Cygwin-X) > Xming (OR Cygwin-X). The service is started successfully when the characteristic graphical X will appear in the Windows tray on the bottom right side of the desktop. NOTE: If the X-window server is not started, the following steps will ultimately fail to launch Mauve successfully. After shut down, restart PuTTY if needed. Then, on the left side of the PuTTY configuration window, navigate to SSH by clicking the small + next to it. Then, navigate into X11 (that has just appeared under the SSH settings) by clicking the mouse on the text. Click active the Enable X11 forwarding checkbox. Navigate back into the Session settings (the top most text in the left side menu). Then connect normally to taito-shell.csc.fi using your credentials from the piece of paper. Upon login to taito-shell.csc.fi, navigate into your working directory:

7 Load the biokit module (module load biokit) and then run the Mauve program: Mauve & Note that the first M of the command is a capital letter. The & ensures you can still use the command-line despite a graphical user interface launches. After checking that the program launches properly, exit the program from the File menu on the top left and clicking Quit. Then exit taito-shell.csc.fi and shut down both PuTTY and WinSCP. Please send all feedback and questions to pashupati.mishra@helsinki.fi You can also post into the Padlet wall at:

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