It was only last March that here at work we’ve updated our machines to Ubuntu 16.04 LTS, just a month before the 2018 edition of the server-ready realease of the Linux distribution that has come to be de ‘de-facto’ standard for Bioinformatics.
I am running mysqltuner to see how the server can be most finely tuned. Unfortunately the package still has problems (ie. in two years the updated version has not been back ported) so I am facing the mysqltuner ERROR 1054 on Ubuntu Server 16.04.
Here’s how I solved it, after a quick digging’ on my search engine:
git clone https://github.com/major/MySQLTuner-perl.git
sudo mv /usr/bin/mysqltuner /usr/bin/mysqltuner.bak
sudo ln -s /opt/MySQLTuner-perl/mysqltuner.pl /usr/bin/mysqltuner
Then I’ve successfully ran my script. Enjoy!
Lately I had to reconfigure an Ubuntu 14.04 server.
Dealing with Tomcat 7 I’ve encountered those two situations:
Enable larger file uploads via Tomcat manager
I had a ~180 war file to deploy. Ubuntu’s Tomcat setting put a limit at 50MB. This has been solved using the tips in this post by skotfred. Unfortunately I haven’t found a more orthodox way of achieving this other than modify the /usr/share/tomcat7-admin/manager/WEB-INF/web.xml in the values max-file-size and max-request-size.
Enable Tomcat monitoring in Munin
Here I’ve followed the tips over this Serverfault discussions.
Adding a [tomcat_ *] was the key.
The other day, after a do-release-update on an Ubuntu box I had some issues with a package which told me:
Errors were encountered while processing:
E: Sub-process /usr/bin/dpkg returned an error code (1)
here’s how I solved:
mv /var/lib/dpkg/info/BROKEN-PACKAGE.* /tmp/
dpkg --remove --force-remove-reinstreq BROKEN-PACKAGE
Sometimes I find myself in the situation of having to lauch some graphical software like synaptic, gedit, baobab while already using the server as root from the command line. I do not want to ‘exit’ my session and use the previous methods of which I’ve written in the past.
This is how I did it.
koolinus@localhost:~$ ssh -Y firstname.lastname@example.org
koolinus@remote:~$ sudo -i
root@remote:~# touch .Xauthority
root@remote:~# xauth merge /home/koolinus/.Xauthority
And that’s all. Now I can launch the needed program without interrupting my root session, for example:
root@remote:~# baobab &
Fwd: Ubuntu 13.10 (Saucy Salamander) released
The Ubuntu team is very pleased to announce the release of Ubuntu 13.10 for Desktop, Server, Cloud, Phone, and Core products.
Codenamed “Saucy Salamander”, 13.10 continues Ubuntu’s proud tradition of integrating the latest and greatest open source technologies into a high-quality, easy-to-use Linux distribution. The team has been hard at work through this cycle, introducing new features and fixing bugs.
Ubuntu 13.10 introduces the first release of Ubuntu for phones and Ubuntu Core for the new 64-bit ARM systems (the “arm64” architecture, also known
as AArch64 or ARMv8), and improved AppArmor confinement. In addition to these flagship features there are also major updates throughout.
Ubuntu Server 13.10 includes the Havana release of OpenStack, alongside deployment and management tools that save devops teams time when
deploying distributed applications – whether on private clouds, public clouds, x86 or ARM servers, or on developer laptops. Several key server
technologies, from MAAS to Ceph, have been updated to new upstream versions with a variety of new features.
Maintenance updates will be provided for Ubuntu 13.10 for 9 months, through July 2014.
To get Ubuntu 13.10
In order to download Ubuntu 13.10, visit:
Recently we’ve decided to move all our CentOS 5 server installations to a more modern, and bioinformatics friendly, environment. So the choose was on Ubuntu, in it’s 12.04 LTS version.
Some commands are different, especially those for exploring packages, their releases and such.
For example to see what packages install $something now I do a:
sudo apt-file search $package
while to see a package’s details, for example nano, I give a:
sudo apt-cache show nano
Maintainer: Ubuntu Developers
Original-Maintainer: Jordi Mallach
Depends: libc6 (>= 2.11), libncursesw5 (>= 5.7+20100313), dpkg (>= 1.15.4) | install-info
Breaks: alpine-pico (<= 2.00+dfsg-5)
Description-en: small, friendly text editor inspired by Pico
GNU nano is an easy-to-use text editor originally designed as a replacement
for Pico, the ncurses-based editor from the non-free mailer package Pine
(itself now available under the Apache License as Alpine).
However, nano also implements many features missing in pico, including:
- feature toggles;
- interactive search and replace (with regular expression support);
- go to line (and column) command;
- auto-indentation and color syntax-highlighting;
- filename tab-completion and support for multiple buffers;
- full internationalization support.
Task: standard, kubuntu-active
That’s all (for now).