Tag Archives: Linux

Linux, Python

Install portal_client on Linux

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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 https://github.com/IGS/portal_client;
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:

https://virtualenvwrapper.readthedocs.io/en/latest/

Linux, Web Server

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

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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;
wget https://dl.eff.org/certbot-auto;
chmod 755 certbot-auto;
./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:

domainname.domain.conf

For example, example.com would be:

example.com.conf

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

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

Then:

mkdir /tmp/static/;

Run certbot:

./certbot-auto certonly

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

game, games, Linux, Ubuntu

Cogs games on Linux not working?

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

http://forum.lazy8studios.com/index.php?PHPSESSID=h1d37r13a2d2ccnk5c5j6b2c94&topic=475.msg837#msg837

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.

~/games/cogs/data/effects/TextureBumpCubemap.fsh

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).

Database, Debian, Linux, Oracle, Ubuntu

Install Oracle SQL Developer on Ubuntu Karmic & Lucid

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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  <http://otn.oracle.com/software/prod‐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:

http://www.oracle.com/technology/software/products/sql/index.html

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/sqldeveloper-2.1.0.63.73-no-jre.zip

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:

/tmp/sqldeveloper_2.1.0.63.73+0.2.3-1_all.deb

See the man page for more information about the tool:

man make-sqldeveloper-package

4. Install the package

sudo dpkg -i sqldeveloper_2.1.0.63.73+0.2.3-1_all.deb

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.

Uncategorized

Kaboom is cool!

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Great tool for converting KDE3 settings to KDE4 on Debian. Also, it’s works well to merge KDE4 settings from .kde4 with KDE3 settings in .kde. This is useful as KDE4 1st used .kde4 to save personal KDE configuration data. KDE4 is now using .kde for config data, which mean early KDE4 users will have problems with new KDE4 apps. Fear not, Kaboom will help!

http://pkg-kde.alioth.debian.org/kaboom.html

I’d advise saving back-up copies of both .kde and .kde4 .

BU Linux, Linux, Red Hat, Ubuntu

Red Hat 9

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I have a Red Hat 9 server that I have to support for a wee while longer. I needed to install some packages and I didn’t have the original install CD’s nor access to Red Hat’s repositories.

After lot’s and lot’s of searching I found the ISO images at:
ftp://archive.download.redhat.com/pub/redhat/linux/9/en/iso/i386/

But, there’s too many users on Red Hat’s FTP server and I can’t get access … thankfully rpmfind.net have a mirror:
http://fr.rpmfind.net/linux/redhat/9/en/iso/i386/

So now I can download the ISO images, and mount them on the Linux box using the loop-back interface and install the packages I need.

I expect to have new hardware within a month or so, and I’ll probably be using BU Linux or Ubuntu 8.04.

Hardware, Laptop, Linux, Tech, Ubuntu

Ubuntu Jaunty & ATI

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This is quick’n’dirty writeup to help others who might have the same problem. I’ll clean this up later in the week …

Ubuntu Jaunty is the new beta version of Ubuntu. It comes with a new version of X.Org and the ATI drivers have been incompatible with this version of X.Org. ATI recently released drivers that support X.Org 1.6. If you have problems with X not starting follow the instructions here:
https://wiki.ubuntu.com/X/Troubleshooting/FglrxInteferesWithRadeonDriver

For me what happened is that X wouldn’t start properly and cause my Lenovo T400 to freeze and lock up. The laptop would boot but when X would start (when the login screen appears) I’d get a black screen with red lines at the top. To solve this I booted to runlevel 1, also known as failsafe mode. If your using a laptop with wireless, I suggest you connect directly to your router using a network cable, otherwise you may have to configure wireless manually (it’s not that hard).

When your system starts, select failsafe mode, on the next screen to appear choose the option to go to a “root shell with networking”.

Next remove the install ATI drivers and install from scratch the ones you need:

sudo apt-get remove –purge xorg-driver-fglrx xserver-xorg-video-ati xserver-xorg-video-radeon
sudo apt-get install xserver-xorg-video-ati
sudo apt-get install –reinstall libgl1-mesa-glx libgl1-mesa-dri
dpkg-reconfigure -phigh xserver-xorg

If this doens’t work for you see the Ubuntu page mentioned above.

Linux, Ubuntu

Xen for Ubuntu Intrepid 8.10

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I was in the process of figuring out and documenting the process of  compiling and installing an Xen enabled kernel on Ubuntu Intrepid 8.10. This was for a specific project that’s not going to come to fruition. I’m not going to bother as I also don’t feel like having my laptop burn a gaping hole through my lap as I wait for the kernel to compile, and well you know I still have some use for the 2 lads downstairs. And after years of compiling kernels, I really can think of more productive uses of my time.

The quickest way is to grab a Debian Xen enabled kernel, this isn’t recommended by Ubuntu and if your not comfortable hacking your system and having to compile modules (drivers in Windows speak) for hardware or proprietary hardware that Debian doesn’t include support for, then don’t even think of doing this and just use KVM.

Here’s how Chris did it for a system running a AMD64 processor, if you’ve an Intel processor you’ll need to use a different kernel:

http://www.chrisk.de/blog/2008/12/how-to-run-xen-in-ubuntu-intrepid-without-compiling-a-kernel-by-yourself/

If you want a later kernel (2.6.27 or 2.6.28) poke around:

http://kernel-archive.buildserver.net/

That’s the approach I’m going to use, as I know that if I’ve problems or issues I’ll be able to figure it out. Anyways, the start of the orignal draft is below, preceded by a minor rant. When I get around to getting Xen on Ubuntu to work with a Debian kernel I’ll add a new post here. Continue reading Xen for Ubuntu Intrepid 8.10 →

Cambridge, Linux

Boston Linux and Unix InstallFest XXXII

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I won’t be able to make it, but if your interested in Linux and are in or around Boston/Cambridge, the BLU is having one of their installfests:

Boston Linux Installfest XXXII
When: Saturday February 28, 2009, 2008 from 9:00 am to 5:00 pm
Where: MIT Building E-51, Room 061
2 Amherst St, Cambridge
Plenty of free parking in front of the building.

What you need to bring: Your computer, monitor, power strips and your
Linux distributions. We do have copies of some distributions.
In general we have expertise with most distros, but if you need special
expertise, please email the BLU discussion list in advance.

COST: It’s free! However, we DO have expenses, and contributions are
welcome. Please consider contributing $25 per machine.

Our volunteers will help you to install Linux on your own system. While
Linux runs on most systems, some systems do have configurations and
hardware that may not be supported. Please consult the following web
pages for hardware compatibility. While we prefer you to bring your own
distros, our volunteers will normally have

Linux.ORG: http://www.linux.org/hardware/index.html
Hardware HOWTO: http://www.linuxdoc.org/HOWTO/Hardware-HOWTO.html
Linux Frequently Asked Questions: http://www.linuxdoc.org/

Generally our volunteers have sets of the latest Fedora, SuSE and
Ubuntu distributions:
* Fedora – http://fedora.redhat.com (Fedora 10)
* Open SuSE – http://opensuse.org (OpenSuSE 11.0)
* Ubuntu – http://www.ubuntu.com (Intrepid Ibex 8.10)
* Debian – http://www.debian.org/

In addition, you can run Linux on your Windows PC through a virtual
machine manager, such as Virtualbox. You can install this in your
Windows machine and run Linux as a guest OS, or install it in your Linux
machine and run Windows as a guest. VirtualBox 2.1
(http://www.virtualbox.org.) is free and is available for Linux, Windows
XP and Windows Vista. Additionally, there are some VMWare clients that
are also free for Windows.

Please refer to the BLU website (http://www.blu.org) for further
information and directions. Parking is available in front of the
building on Amherst St. Enter the building, and take the elevator to
your left down 1 floor. Room 061 is opposite the elevator.