More On The Virtues Of VirtualBox – ACID (or AICD) Under Ubuntu 14.04 (By Way Of OpenSuse 11.2)

“Stop that!” – George Carlin

If you’ve obtained source code from an academic lab that was last developed some time ago and you spent a whole day installing libraries and symbolic links and redefining variables in your .bashrc and downgrading libraries and redefining paths and have 20 tabs open in your browser that all go to 20 different obscure error discussions on Stack Overflow and it’s late and you’re tired and you think you might not need the program after all if you do a bunch of other workaround things instead – what’s below is for you.

Academics have been developing small code for (nearly) millions of years to make their lives easier – and we all benefit when that code is made available to others (esp. when it helps in data analysis). When that code is a series of perl or python scripts, there’s generally little reason why you should have any run issues. When they call on external libraries or specific tools, generally that information is available in the README somewhere. Generally speaking, there’s no reason why a code shouldn’t work in a straightforward manner when the developer doesn’t make it known that something else needs be installed to make it work.

So, why doesn’t code A work on your linux box? A few possibilities.

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OrthoDB 1.6 Installation On Ubuntu 14.04 (And Related) – Build Errors And The Simple Fixes

UPDATE: 20 May 2016 – With thanks to OrthoDB’s very own Fredrik Tegenfeldt, here’s a more distro-complete fix for the Makefile.rules file.

# BRH flags
ifeq ($(USE_BRH),1)
BRH_DIR        = $(BASE_DIR)
CPPFLAGS    += -I$(BRH_DIR)/src
ifeq ($(WITH_RPATH),1)
LDFLAGS        += -L$(LIB_DIR) -Wl,-rpath,$(LIB_INSTDIR)
LDFLAGS        += -L$(LIB_DIR)
LDLIBS        += -lbrh

ifeq ($(USE_BOOST_THREAD),1)
LDFLAGS        += -pthread
LDLIBS      += -L$(DIR_BOOST_LIB) -lboost_system -L$(DIR_BOOST_THREAD) -l$(LIB_BOOST_THREAD) -lpthread

And Happy New Year,

Yet another random Ubuntu-centric bioinformatics aside in the event others run into the same build issues (with errors included below, as you likely googled those first). For those wondering…

The Hierarchical Catalog of Orthologs v8

Orthology (website, download) is the cornerstone of comparative genomics and gene function prediction. OrthoDB aims to classify protein-coding genes from the increasing number of available sequenced genomes into groups of orthologs descended from a single gene of the last common ancestor (LCA) of each clade of species. Applying this concept to the hierarchy of LCAs along the species phylogeny results in multiple levels of orthology: the more closely-related the species, the more finely-resolved the orthologous relations.

The build here was on a fresh installation of 64-bit Ubuntu 14.04 (Trusty Tahr). All of the errors produced come from running on that clean install, meaning you’ll run into dumb errors (like missing build-essential), didn’t-know-we-needed-that errors (boost), and that’s-probbly-an-Ubuntu-oddity errors (with a modified Makefile.rules file with explicit boost calls linked to below; I suspect the developers are working on a non-Ubuntu distro).

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GROMACS 5.0.x CUDA/GPU Detection Failure With Ubuntu 14.04 nVidia 331.113 Update – Fix With An apt-get

If not for the near-20x speedup I’ve achieved running GROMACS on an nVidia GTX 770 Classified over an Intel i7 Extreme 6-core, nVidia in Ubuntu would almost be more trouble than its worth. The initial installation of the nVidia drivers from the nVidia website works, then the first time Ubuntu auto-updates the drivers to the latest-and-greatest, you’re never entirely sure what the next boot is going to look like – usually a black screen at best. And, if you found this page while looking for a solution to the nVidia driver update black/blank screen, my solution (which has worked without issue to date) is to ditch lightdm and use the GNOME Display Manager (gdm) instead (this apparently appears to be a theme with Ubuntu 14.04 installs on SSD drives as well).

sudo apt-get install gdm

Now, with that settled, the latest update (331.113) broke my GROMACS GPU install (performed using the steps outlined at: GROMACS 5.0.1, nVidia CUDA Toolkit, And FFTW3 Under Ubuntu 14.04 LTS (64-bit); The Virtues Of VirtualBox). The error for my system looks as follows:

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CudaMiner Installation In Ubuntu 12.04 LTS Using CUDA Toolkit 5.5 And “Additional NVIDIA Drivers”

Author’s Note 1: It is my standard policy to put too much info into guides so that those who are searching for specific problems they come across will find the offending text in their searches. With luck, your “build error” search sent you here.

Author’s Note 2: It’s not as bad as it looks (I’ve included lots of output and error messages for easy searching)!

Author’s Note 3: I won’t be much help for you in diagnosing your errors, but am happy to tweak the text below if something is unclear.

Conventions: I include both the commands you type in your Terminal and some of the output from these commands, the output being where most of the errors appear that I work on in the discussion.

Input is formatted as below:

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Brief Update: Amber 11 And AmberTools 1.5 In Ubuntu 12.04 LTS

This post is a brief update to a much longer and more involved discussion of Amber 11 and AmberTools installation in Ubuntu 10.04 LTS (Lucid Lynx) (as the changes are minor and the parallelization setup remains largely the same). You can find this more involved discussion at

Long/Short – the installation under Ubuntu 12.04 LTS (Precise Pangolin) is not much different and goes without hitch provided you keep your locations organized. NOTE 1: I’ve not a copy of Amber12, so cannot speak for any changes to its installation procedure. NOTE 2: This install assumes 32-bit only.

Updated Procedure

If you tried installing all of the build software from the 10.04 LTS post, you’ll receive errors like the following (as usual, I include error messages for those who are searching against error messages)…

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Abinit 6.8.1 In Parallel With OpenMPI 1.4.1 In Ubuntu 10.04.2 LTS (And Related)

It has been a banner week for Ubuntu installations.

The installation of Abinit 5.6.5 with OpenMPI 1.3.1 (previously reported at wasn’t bad, but several games had to be played (at the time) to make everything compile and run correctly. I’m pleased to report that Abinit 6.8.1 and OpenMPI 1.4.1 seem to play better together, this simplified considerably over the previous installation guide by the use of the apt-get version of OpenMPI 1.4.1. A bit of option calling in the configure step is needed (and the errors for not doing it are included below).

0. For the Antsy Copy+Paste Crowd

Commands below.

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Amber 11 And AmberTools 1.5 In Ubuntu 10.04 LTS (And Related, Including A How-To For EOL 8.10)

Having successfully navigated serial and parallel Amber10 installs under Ubuntu 8.10, I am pleased to report that the process for Amber11 with OpenMPI (from apt-get, one doesn’t have to build from scratch) under Ubuntu 10.10 is seemingly much easier (and have it here so I don’t forget). There is a bit of persnicketiness to the order of the serial and parallel installs that must be kept track of (and I’m building in serial-to-parallel order), but the process is otherwise straightforward.

For organizational purposes, I’m building amber11 in my $HOME directory. This removes some of the PATH issues with sudo-ing aspects of the install (and can be moved into another directory after the build is complete).

1. apt-get Installs

The search for dependent programs and libraries is a long and involved one given how many programs I have installed. Therefore, instead of trying to find all of the amber-dependent installs for successful building, I’m simply providing the list of everything I have on the test machine. As hard drives are cheap and Ubuntu will warn of conflicts, I recommend simply installing the below and accepting the 100 Mb hit to NOT have to find the smallest apt-get set (yes, some of these are obviously not needed).

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bfast-0.6.5a, MUMmer-3.22, and Amos-3.0.0 Installs In Ubuntu 10.04 LTS (And Related)

Taking care of a DNA/RNA fragment alignment installation triple-threat with this post. These Ubuntu installs for largely problem-free, but one little trick is needed for Amos (this because of my use of “/opt” for my usual installation and compilation attempts and, more so, my not being interested in modifying the root PATH statement despite the constant use of sudo when building in “/opt”).

So, with the downloads of

bfast-0.6.5a (currently:
MUMmer-3.22 (currently:
Amos-3.0.0 (currently:

taken care of, the following process is performed.

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/var/lib/ureadahead/debugfs And Disk Space “Recovery” In Ubuntu 10.04

And happy new year.

I had thought this was something involving Gaussian09 memory usage until I restarted a machine and found the same problem occurring in Ubuntu. Below is a quick fix (and reminder for the future).

Checking disk space with df -all :

user@machine:~$ df -all
Filesystem           1K-blocks      Used Available Use% Mounted on
/dev/sda1            147550696   5863896 134191632   5% /
proc                         0         0         0   -  /proc
none                         0         0         0   -  /sys
none                         0         0         0   -  /sys/fs/fuse/connections
none                         0         0         0   -  /sys/kernel/debug
none                         0         0         0   -  /sys/kernel/security
none                   3053752       260   3053492   1% /dev
none                         0         0         0   -  /dev/pts
none                   3058264         0   3058264   0% /dev/shm
none                   3058264        84   3058180   1% /var/run
none                   3058264         0   3058264   0% /var/lock
none                   3058264         0   3058264   0% /lib/init/rw
none                         0         0         0   -  /var/lib/ureadahead/debugfs
nfsd                         0         0         0   -  /proc/fs/nfsd
binfmt_misc                  0         0         0   -  /proc/sys/fs/binfmt_misc

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Maq-0.6.x Or Maq-0.7.x (And Likely Others) Installation In Ubuntu 10.04 LTS (And Likely Others)

So, with the BclConverter installation complete and a small QSEQ-to-FASTQ script available to convert the QSEQ output, the/a next step is the alignment of your lane-worth of sequenced DNA. The Maq program is used by the Cornell Sequencing Center (and was recommended as the workhorse tool for this task) and is available by link from the Illumina third-party tools list. In keeping with my no-interest-in-installing-another-distro run of Ubuntu luck, the procedure below explains the process of building Maq using as much apt-get as possible. In the case of Maq, there is one small busy step in the installation process because we need a copy of local that is NOT available by some easy package install (although what one has to do isn’t terribly difficult either and I’ve linked local copies of the two .deb files below).

Installation Procedure

The process begins with apt-get, continues to dpkg, and then is finished with an easy make.

1. apt-get Install List

The official package list, I am quite sure, is below. From a Terminal window:

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