Tomcat 7, munin and Ubuntu 14.04

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.

solving DESeq2 installation issues

At work a colleague asked me to do a system-wide installation of the R module DESeq2 in one of our internal servers.
The installation procedure is quite straight-forward:

source("http://bioconductor.org/biocLite.R")
biocLite("DESeq2")

Unfortunately I had some issues on my system, in fact I got:

…
Warning in fun(libname, pkgname) :
couldn't connect to display "localhost:12.0"
* DONE (maSigPro)

The downloaded source packages are in
	‘/tmp/RtmpfdD2RC/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘annotate’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status

I then tried to install manually the various dependencies, like XML. Still no luck. After a quick Google search I found that I was missing a couple of -dev packages on my Ubuntu machine, so I installed them:

root@server:~# apt-get install libcurl4-openssl-dev libxml2-dev

… and then re-tried to install DESeq2. This time everything was ok. Problem solved!

using graphical software on Ubuntu as root after you’ve logged in remotely

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 koolinus@remote.server.it
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 &