Changes between Version 4 and Version 5 of FrequentlyAskedQuestions

Timestamp:

Jul 5, 2011, 12:43:42 PM (13 years ago)

Author:

Patrik Söderström

Comment:

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FrequentlyAskedQuestions

@@ -2 +2 @@
 Please add questions here if you think the answer is relevant to other users.
 
-1. How do I login to the grid?
+'''1.''' How do I login to the grid?
 To login, open either Terminal (Mac) or Putty (PC) and type in the following command:
 ssh -Y username@my-mgrid.mykopat.slu.se
 Remember your username is the same as your AD account . You will be prompted for your password, just enter your AD password.
 
-2: How do I start my job in the queuing system?
+'''2.''' How do I start my job in the queuing system?
 To start your job in the queuing system please refer to the following guide. 
 In brief, you will create a script file that will contain the information needed to run your job, including a command to start whatever program you want to run with its parameters. The script also contains information on your email address, what folder to run the program in , how much time the job will need and how much memory the job will need (RAM).
 
-3: How do I start an interactive job using the queue system for programs like: [wiki:Blast2Go], [wiki:Tablet] and [wiki:Mothur]?
+'''3.''' How do I start an interactive job using the queue system for programs like: [wiki:Blast2Go], [wiki:Tablet] and [wiki:Mothur]?
 To start these types of programs you must first get a VNC (Virtual Network Computing) session opened in Terminal or Putty. 
 Logon to the grid as you would do normally and once the prompt is up, type in the command '''vncserver'''.
@@ -19 +19 @@
 A VNC window should open up and you will be in the Debian GUI (Graphical User Interface). You can then go into Applications/Terminal in the GUI and run Blast2Go, Tablet or Mothur.
 
-4: How do I transfer files between my computer and my grid home folder?
+'''4.''' How do I transfer files between my computer and my grid home folder?
 To transfer files, you can use either Terminal/Putty or a GUI program such as Fugu/WinSCP. To transfer in Terminal/Putty use the copy command - cp, 
 (for example: cp filename source folder/filename destination). In Fugu/WinSCP you connect to the server and basically drag and drop like in Finder and Explorer.
 
-5. Can I drag and drop files in Fugu and WinSCP?
+'''5.''' Can I drag and drop files in Fugu and WinSCP?
 You can drag and drop files within Fugu and WinSCP but not directly from your desktop to either program. You must have either program setup so that there are two windows so you can select a source on one side and destination on the other.
 
-6. How do I start the program Velvet, or any other program on the grid for that matter?
+'''6.''' How do I start the program Velvet, or any other program on the grid for that matter?
 To start programs on the grid, most of the manuals have commands that are usually used in starting the programs. However, on our grid, we have simplified the process somewhat and most of the time you will only need to type in the program name to get it to start.
 For example -
@@ -34 +34 @@
 This is also the case with running any specific scripts - you will not need to use " ./ " before the script name to get it to run.
 
-7. How do I start Mr. Bayes as an interactive job in the queue?
+'''7.''' How do I start Mr. Bayes as an interactive job in the queue?
 To start Mr Bayes in the interactive queue, at the prompt you type in the command qrsh. This will start a job in the queue, please note you must ask for a run time and RAM allocation just as you would with a regular job request. Once the session is open in another shell, you would simply run the program Mr Bayes by going into the directory where you have the program and your data files and start the program. 
 
@@ -45 +45 @@
 
 Please refer to this guide for an example.
-8. How do I run the shuffleSequences_fastq.pl script under Velvet?
+
+'''8.''' How do I run the shuffleSequences_fastq.pl script under Velvet?
 This script has been replaced in our sytem with the script shuffleSeqs. Simple type in the script name "shuffleSeqs" at the prompt and it will show you the input format to use.