Monthly Archives: December 2017

Adventures in Linux hosting: Misc. setup with apt

After setting up the new home linux box on Xmas eve, I’ve been gradually building it up to be a test bed for things I do at work. The apt package manager makes this pretty easy so far, compared to what I’ve done in the past.


Sorry vim folks, I prefer emacs for shell based editing (actually, I prefer BBEdit, which I can do via SFTP, but there are times when a local editor makes more sense).

sudo apt-get install emacs


This is a Cisco-compliant VPN client, which I’ll need if I want to connect through the firewall.

sudo apt-get install vpnc

This installs but I can’t seem to get a connection to TAMU’s vpn server. This may not be needed, though, since the TAMU enterprise Github doesn’t need VPN


I could have done this in the software selection but let’s go ahead and set up a basic LAMP webserver:

sudo apt-get install lamp-server^

The ^ character is required. This installs mysql, apache, and php7.0.  The html root appears to be in /var/www/html


  • sudo apt-get install phpmyadmin php-mbstring php-gettext


Yes, jbrowse is the new thing, but there are still some things I want to migrate from gbrowse. And there’s an apt package!

sudo apt-get install gbrowse

Important note, the URL is for gbrowse2! In my case, it’s http://<IP>/gbrowse2/

To do updates

I thought I had set it up to do this automatically, but it isn’t. So…

sudo apt update
sudo apt upgrade

Adventures in Linux hosting: Getting Ubuntu onto my home Dell T30

My MacBook is between the new Dell T30 and my monitor. You can see the USB stick attached to the MacBook where I burned the ubuntu ISO

Thanks to the USPS for delivering on a Sunday. The new T30 arrived today at around 10AM. As I suspected, the contents are just the main box and a power cord. I went to Best Buy and picked up the cheapest USB2 keyboard and mouse I could find (there were probably some of these lying around the lab, but I bought new). I borrowed the HDMI cable we were using for the Apple TV, and hooked up to a monitor.

Cntrl-alt-delete reboots. Holding down F2 gives the Dell system management software.

Set up a USB stick for installation

I found the basic installation documentation kind of confusing. So I started with the steps in this tutorial: Create a bootable USB stick, on macOS.

  • Download Ubuntu Server 16.04.3 LTS from:
  • Download Etcher. This is recommended for burning the image onto the USB stick. When Etcher is done, the MacBook complains about the inserted media not being readable. Just eject it.

Putting this stick in the USB port didn’t allow it to boot. But a clue comes from the last screenshot of the tutorial where the stick is shown as an EFI boot. Changed the Dell to look for UEFI boot. Now I get an installation option for Ubuntu when I reboot.

  • Used defaults except
    • to unmount before writing partitions.
    • automatically do security updates
  • Network failed until I plugged an ethernet cable into the back connected to the Airport Time Capsule.
  • Software selection
    • standard system utilities
    • OpenSSH server

After doing this and rebooting, I had to go back to the Dell system config to switch back to legacy boot instead of UEFI. But once I had done that, I get a boot into Ubuntu and I can ssh in using the local IP address.

Shut it down to move it to a better location in the living room instead of the dining room table. Now it’s running with no keyboard, mouse, or monitor and I can ssh into it from my MacBook.

Update: The Dell documentation talks about using their LifeCycle Controller to install an OS. But this doesn’t seem to come on the T30.

Adventures in Linux hosting: Development setup at home

One option to do my self-designed Linux education would be to do everything in VMWare. But while I’ve done that in the past, it hasn’t taught me what’s going on when we’ve had problems with our existing boxes where the IT people tell me that they had to do something with the kernel, or when I’ve had to reboot and watch the stream of warnings or worse on the local monitor before Ubuntu even loads.  I suspect that some of that has to do with a long-gone IT employee screwing up the initial installation, but I’d like to understand it better.

So, with computers being reasonably cheap, I decided it would be fun to set up a version of our websites on our home wifi network, not accessible to the outside world. Yesterday I ordered a Dell PowerEdge T30 Business Mini Tower Server System, and was pleasantly surprised that it had free shipping to arrive on Christmas Eve. The system comes with 8 Gb of RAM and a 1T HD. Eventually, I will probably upgrade both of those if I can (I think it’s possible with this model), but even with that base configuration it’s comparable to what we are currently using on our Macs. 

Debby has gone to visit family, leaving me to look after the cats in Texas. This will be an opportunity for a nerdy Xmas break! Off to read Ubuntu manuals


The first question even before the thing arrives is about the appropriate installation. The Pentium G4400 dual core processor on the box I ordered is cheaper than the Xeon alternative. It seems that it falls under the Intel EM64T category of processors, even though the string “EM64T” doesn’t show up on the Intel page for that CPU.

Time for me to get more serious about Linux

My group started into bioinformatics thanks to former students Hai Zhu and Leonardo Marino-Ramirez, who set up the first LAMP webserver in the lab, a box they made that we called Being Mac users, we thought that the Unix roots of OSX would be useful in the transition to doing informatics and web-based resources, so I purchased a G5 XServe  which started a series of machines we named based on protein quaternary structure. It was called As the EcoliHub/PortEco/EcoliWiki projects got funded and we got some stimulus money to work on B. subtilis, we gradually added to our collection of machines. trimer and tetramer were intel XServes. hexamer was the last version of the Apple Intel Xserve shipped by Apple. Meanwhile pentamer and heptamer were linux boxes running Ubuntu. For the most part the heavy work was done on the Macs, and we even moved GONUTS to run on a mac mini after one of the Intel Xserves died.

One of the things I liked about the XServe setup when we first got dimer was the way we could do server administration via the Server Admin and Workgroup Manager apps. But as the machines aged, and the older ones were not supported on newer OSX versions, Apple did something annoying: they made Server Admin incompatible with older OSX releases, even though it was pretty obvious that it was just a pretty front end to send unix commands and show the outputs in the GUI. So I gradually started learning how to do various system admin tasks via the terminal; there are some I’ve never figured out how to do completely without the GUI, though.

The rack mountable blade servers stopped supporting updates with Snow Leopard. We’ve kept the TAMU IT security people at bay by running MacPorts to replace obsolete packages, but it’s gotten to the point where time to give up on the Mac servers and migrate everything to Linux. My department prefers Ubuntu, so that’s the way I’m going to go.

In the long run I expect we will move from our own hardware to A&M server virtualization or maybe something like Amazon. But for now, I’m not comfortable with the capability and price for our own hosting, and there are issues with URLs and domains for moving some of our sites off campus.