(r4) Barrick Lab :: ProtocolsUnixCommandsQuickReference

---+ Unix Commands Quick Reference
Useful commands and flags that we get tired of looking up...

---++ Disk Space
The <code>du</code> command is verbose and confusing if you run it without options. Here is how to get a human-readable output and a grand total for the path argument (omit for current directory).

<code>du -hc</code>

---++ Fixing Line Endings
If you get odd errors after transferring a text file from a PC or Mac to a Unix machine, it's likely that you have a problem with [[http://en.wikipedia.org/wiki/Newline][newline characters]]. This is especially common when editing files in Excel and saving them to tab-delimited or comma-delimited files for input into. You can generally avoid this problem and fix the line endings by using an industrial strength text editor. This command converts Mac line endings in a saved Excel file to Unix line endings.

<code>tr "\r" "\n" < input.tab >.converted.tab</code>

---++ Merging commands to be serial on TACC

Sometimes you have 96 short jobs that you want to run serially 8 at a time on 12 cores rather than requesting 96 cores. This command will combine every 8 lines in a file into one line separated by && so that these commands are now run on one core.

<code>paste -s -d'#######\n' commands | sed "s/#/ \&\& /g" > commands8</code>

---++ Adding your path to the command prompt

Add to your <code>.bashrc</code> or similar bash startup script:

<code>export PS1='\w\$ '</code>

Barrick Lab > ComputationList > ProtocolsUnixCommandsQuickReference

Contributors to this topic

JeffreyBarrick, LucyLeblanc

Topic revision: r4 - 2016-02-29 - 21:09:40 - Main.JeffreyBarrick