Category Archives: Linux

Install portal_client on Linux

A user asked for help installing Portal Client. Which is a:

Python-based client for downloading data files hosted by the an instance of the portal software developed by the GDC and further modified by the Institute for Genome Sciences (IGS)

You can install this in any directory that you have write permissions to, and you will need python3 installed.

Here are the quickie install instructions:

git clone;
python3 -m venv --copies VENV_portal_client;
source VENV_portal_client/bin/activate;
pip install -r portal_client/requirements.txt;
cd portal_client;
easy_install . ;

Any time you need to run the tool, source the Python Virtual Environment (virtualenv) and run the command. For example:

source VENV_portal_client/bin/activate;
portal_client --help;

If you use a lot of Python virtualenv’s, I suggest using the virtualenvwrapper tool, which makes it easier to manage and run many virtualenv’s:

VAST Storage API & JQ

Glendalough Hiking Trail
Hiking Glendalough Park in Ireland

Vast builds some neat storage systems that provide management functionality via a REST API.

jq is a command-line JSON processor, or as the author describes it “sed for JSON”.

This is how I use both tools to get a quota’s used capacity:

curl -u $USERNAME:$PASSWORD --insecure -X GET "https://your-vast-dashboard/api/quotas/" -H "accept: application/json" | jq  ".[]|select(.used_capacity_tb | length > 0) | {name: .name, used: .used_capacity_tb}" 

USERNAME and PASSWORD are environmental variables set to the username and password you use to access your VAST API. Change to URI to point to your VAST appliance.

Edx on Debian Stretch

Edx on Debian Stretch

After you clone the Edx repo there you will find a (undocumented) list of packages required to install on Ubuntu:


These packages and others are required for Debian Stretch.  First, install these packages:

sudo apt-get install $(grep -vE "^\s*#" requirements/system/ubuntu/apt-packages.txt   | tr "\n" " ")

And then install these packages:

sudo apt-get install python-scipy python-numpy build-essential python-dev gfortran libfreetype6-dev libjpeg-dev libtiff5-dev zlib1g-dev libpng-dev  libxml2-dev libxslt-dev yui-compressor graphviz libgraphviz-dev graphviz-dev mysql-server libmysqlclient-dev libgeos-dev libreadline7 libreadline7-dev mongodb nodejs mysql-client virtualenvwrapper libgeos-ruby1.8 lynx-cur libxmlsec1-dev swig  libsqlclient-dev libxmlsec1

Like the photo? See a bigger version on Flickr.

Let’s Encrypt Cert & Nginx (Using a Web Proxy) on Centos 6.x

Let's Encrypt Cert & Nginx (Using a Web Proxy) on Centos 6.x

This was done on Centos 6 where prebuilt ‘certbot’ packages are not available. On Centos 7, install ‘certbot’ from the EPEL repo.

cd ~root;
mkdir certbot;
chmod 755 certbot-auto;

This installs packages, including gcc, which you may want to uninstall as it’s bad practice to have compilers on a external facing (public) Web server.

On my server I have a different configuration file for each server we’re proxying for. These are in /etc/nginx/conf.d/ and using a naming convention of:


For example, would be:

Edit your config file and add this after location / { … } :

location /.well-known {
alias /tmp/static/.well-known;


mkdir /tmp/static/;

Run certbot:

./certbot-auto certonly

Continue reading Let’s Encrypt Cert & Nginx (Using a Web Proxy) on Centos 6.x

Build & Install Osra 1.3.8 on Ubuntu 11.10


Osra is a a utility designed to convert graphical representations of chemical structures create by Igor Filippov at the National Cancer Institute. This page documents how to compile and install Osra on Ubuntu Linux 11.10. These instructions may work on other versions of Ubuntu Linux and on Debian Linux.  Please leave a comment if you have compiled Osra using these instructions on a different version of Ubuntu, or on other Linux distributions.


At the time of writing this doc, March 2012, the Osra version is 1.3.8 and is available at:

I copied all the source to a directory in /tmp. If you need the source code at some later point in time, don’t use /tmp as files in /tmp are deleted upon reboot (if they’re older than 14 days). Also, at the time of writing Osra requires a patched version of Gocr for Osra to work. You need to install Gocr before you try to compile and install Osra, you also need to install other packages required for Osra to compile. Most are listed below, but see the Osra Homepage for more details.

An overview of the steps are:

  1. Install required Ubuntu packages
  2. Compile and Install Gocr
  3. Compile and Install Osra

I’ve also written instructions on how to install Osra 1.2.1 on Ubuntu 9.04, however that was written in 2009. Continue reading Build & Install Osra 1.3.8 on Ubuntu 11.10

Cogs games on Linux not working?

See this forum posting for a potential fix, if your using an ATI graphics card:

This is a fix for the bug where Cogs launches with the following output:

Shader compile log for data/effects/TextureBumpCubemap.fsh:
Fragment shader failed to compile with the following errors:
ERROR: 0:41: error(#132) Syntax error: ‘smooth’ parse error
ERROR: error(#273) 1 compilation errors.  No code generated

Apparently the word “smooth” is reserved, but only on ATI cards in Linux.  The fix is to modify the following file.


Just do a global replace of the word “smooth” with “Smooth”.

A huge thanks to Renee Marie Jones, who figured this one out :)

I wasn’t seeing that particular output on the console, and the screen was just blank/black and I could hear the music. But, this fix did work for me on Ubuntu Linux 10.10 (Maverick).

Install Oracle SQL Developer on Ubuntu Karmic & Lucid

If you want to install Oracle’s SQL Developer on Ubuntu (or another DEB based system such as Debian) you can do one of the following:

  1. Download the RPM package and install using rpm (not advisable).
  2. Download the RPM package and convert to a DEB package using alien
  3. Download the ZIP file titled “Oracle SQL Developer for other platforms” and manually install
  4. Use the make-sqldeveloper-package to convert the ZIP file into a DEB package

I used the make-sqldeveloper-package, which is available for Debian and Ubuntu and it’s derivatives. However, the man page and the instructions are little unclear on how to use it. You need to download the zip file available at Oracle’s (and not the RPM file nor any of the other packages) and then use the make-sqldeveloper-package to convert it to a DEB which you can then install using the dpkg command.

This is preferable to using rpm or alien as you can more easily manage the package using Debian’s and Ubuntu package management tools, plus it will integrate SQL Developer into Gnome’s Menu System . Plus, when Oracle updates their version you can use make-sqldeveloper-package to create an updated DEB package and easily update the version you have installed. The procedure outlined below works on Ubuntu Karmic and should also work on any Debian version that has the make-sqldeveloper-package.

As the man page states:

This utility will require you to download the “Oracle  SQL  Developer  for  other  platforms”  archive  from  <‐ucts/sql/> to create the Debian package from.

1. Download the ZIP file from Oracle’s site

You will need to accept Oracle’s license agreement and download the ZIP file, titled “Oracle SQL Developer for other platforms”, from:

2. Install the make-sqldeveloper-package package

sudo apt-get install sqldeveloper-package

You will need Ubuntu’s multiverse software repository. See the instructions on how to do so.

2.a. Install the tofrodos package

sudo apt-get install tofrodos

Create symbolic links to the tofrodos commands to allow the sqldeveloper-package to work:

sudo ln -s /usr/bin/fromdos /usr/bin/dos2unix
sudo ln -s /usr/bin/todos /usr/bin/unix2dos

Thanks to Miles for the tofrodos tip.

3. Convert the ZIP file to .DEB package

The format of the command is:

make-sqldeveloper-package -b BUILD_LOCATION LOCATION_OF_ZIP_FILE

In my example, I’m going to use /tmp/ORA as the build location and the ZIP file has been download to my Desktop (~Desktop).

make-sqldeveloper-package -b /tmp/ORA/ ~/Desktop/

The command will create the build directory and remove it when the command finishes. If the command completes successfully you’ll see the following output after a minute or two:

make-sqldeveloper-package: Building sqldeveloper package in "/tmp".

The DEB file will be created in the current directory. In my example I had changed directories to /tmp and that’s where the DEB file will be:


See the man page for more information about the tool:

man make-sqldeveloper-package

4. Install the package

sudo dpkg -i sqldeveloper_2.

5. Run SQL Developer

After installing there should he an entry in Gnome’s menu to start the SQL Developer. It’s located under:

Applications->Programming->SQL Developer

Note: You will need a JVM installed for the tool to run.

Obligatory Screen Shot:

Oracle SQL Developer

Updated September 27th 2010. Added instructions from Miles on installing dos2unix alternative for Ubuntu Lucid. The dos2unix command is not available in Ubuntu Lucid.

Compiling EIGENSOFT on Ubuntu Januty

These are rough notes on how to compile Eigensoft 3 on Ubuntu Jaunty.

Update, Eigensoft 4 is available and should compile on more recent versions of Ubuntu:

Create a location to build the code:

Warning: /tmp is for temporary files, and any files & directories you create there will be remove upon some subsequent reboot.

cd /tmp;
mkdir EIGEN;
cd  EIGEN;

Get the Eigensoft source code:

tar xzvf EIG3.0.tar.gz;

Install required dependences: Continue reading Compiling EIGENSOFT on Ubuntu Januty