https://divingintogeneticsandgenomics.com/tags/ubuntu/ Recent content in Ubuntu on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Thu, 13 Jul 2017 13:42:00 -0700 https://divingintogeneticsandgenomics.com/archive/mount-smb-on-ubuntu/ Thu, 13 Jul 2017 13:42:00 -0700 https://divingintogeneticsandgenomics.com/archive/mount-smb-on-ubuntu/ View this gist on GitHub https://divingintogeneticsandgenomics.com/archive/install-gimp-2-8-in-ubuntu-12-04/ Wed, 21 Aug 2013 15:30:00 -0700 https://divingintogeneticsandgenomics.com/archive/install-gimp-2-8-in-ubuntu-12-04/ I was trying to make some figures, and google told me GIMP is a very popular software as an alternative to Photoshop. Ubuntu 12.04 has GIMP 2.6 installed. To update to GIMP 2.8, follow the instructions here: http://www.maketecheasier.com/upgrade-to-gimp-2-8-in-ubuntu/2012/05/04 and install the plugins: http://www.webupd8.org/2013/02/gimp-284-released-install-it-in-ubuntu.html It takes long time to make a good-looking figure. I will write a post to demonstrate how to make a heatmap by R next time. https://divingintogeneticsandgenomics.com/archive/install-bioawk-in-unbuntu/ Sat, 20 Jul 2013 20:21:00 -0700 https://divingintogeneticsandgenomics.com/archive/install-bioawk-in-unbuntu/ Bioawk is written by Heng Li, and it can handle formats like: bed: 1:chrom 2:start 3:end 4:name 5:score 6:strand 7:thickstart 8:thickend 9:rgb 10:blockcount 11:blocksizes 12:blockstarts sam: 1:qname 2:flag 3:rname 4:pos 5:mapq 6:cigar 7:rnext 8:pnext 9:tlen 10:seq 11:qual vcf: 1:chrom 2:pos 3:id 4:ref 5:alt 6:qual 7:filter 8:info gff: 1:seqname 2:source 3:feature 4:start 5:end 6:score 7:filter 8:strand 9:group 10:attribute fastx: 1:name 2:seq 3:qual 4:comment  I followed the tutorial here https://github.com/vsbuffalo/bioawk-tutorial https://divingintogeneticsandgenomics.com/archive/ubuntu-12-04-networking-restart/ Sat, 20 Jul 2013 15:39:00 -0700 https://divingintogeneticsandgenomics.com/archive/ubuntu-12-04-networking-restart/ If I suspend my computer at school, I can not connect to the internet when I get home. I searched on line and found the command at terminal: /etc/init.d/networking start but it did not work, it says the command is deprecated.... Instead, type tommy@tommy-ThinkPad-T420:~$ ifconfig eth0 Link encap:Ethernet HWaddr 00:21:cc:71🆎50 UP BROADCAST MULTICAST MTU:1500 Metric:1 RX packets:0 errors:0 dropped:0 overruns:0 frame:0 TX packets:0 errors:0 dropped:0 overruns:0 carrier:0 collisions:0 txqueuelen:1000 RX bytes:0 (0. https://divingintogeneticsandgenomics.com/archive/book-recommendation-sed-awk-101-hacks/ Mon, 01 Jul 2013 18:38:00 -0700 https://divingintogeneticsandgenomics.com/archive/book-recommendation-sed-awk-101-hacks/ I highly recommend this book for text manipulation http://www.thegeekstuff.com/sed-awk-101-hacks-ebook/ Through my limited experience of "bioinformatics", I realized that we spend a lot of time to reformat the data ( mostly in txt format) to some other formats which can be fed into other programs. python has a very good re (regular expression) module for that purpose, but I do like the one liner of Sed and Awk. Sometimes, I am just too lazy to write something like: https://divingintogeneticsandgenomics.com/archive/run-ape-plasmid-editor-in-linux/ Wed, 29 May 2013 08:06:00 -0700 https://divingintogeneticsandgenomics.com/archive/run-ape-plasmid-editor-in-linux/ I used to like APE on windows. I want to run it on linux (ubuntu 12.04 LTS) also. A quick google search: http://www.allandebono.org/ubuntu,ape/plasmid-editor/ I followed the instruction. first download the APE for linux here http://biologylabs.utah.edu/jorgensen/wayned/ape/Download/ unzip it, you will find two folders, one for Linux, the other one for Mac_OS copy the "APE linux" folder to your home directory: /home/tommy/APE_linux. I rename it as APE_linux, as linux "hates" the empty space. https://divingintogeneticsandgenomics.com/archive/check-file-and-folder-size-in-linux/ Sat, 30 Mar 2013 20:49:00 -0700 https://divingintogeneticsandgenomics.com/archive/check-file-and-folder-size-in-linux/ How to check file and folder size http://www.cyberciti.biz/faq/how-do-i-find-the-largest-filesdirectories-on-a-linuxunixbsd-filesystem/ How do I find the largest top files and directories on a Linux or Unix like operating systems? Sometime it is necessary to find out what file(s) or directories are eating up all your disk space. Further, it may be necessary to find out it at the particular location such as /tmp or /var or /home. There is no simple command available to find out the largest files/directories on a Linux/UNIX/BSD filesystem.