Few things to note before we begin.
- This guide assumes you are using Ubuntu 10.04 LTS Maverick. It may work under other versions, but only tested in 10.04
- The versions of staden and io_lib that were used are
1. Easiest thing to do is create a folder in your home directory called staden and do everything inside there
mkdir ~/staden
cd ~/staden
2. Download both staden and the staden-iolib packages from here. I use wget but you can do it however you want. Just make sure to save them to ~/staden
3. Upack the two files. You should have one that is something like staden-2.0.0b7-src.tar.gz and the other is io_lib-1.12.5.tar.gz
for file in `ls *.gz`; do tar xzvf $file; done;
4. Now we need to setup your system so it has the prerequisites for compiling as well as for staden
sudo apt-get install tclx8.4 tclx8.4-dev tk8.4 tk8.4-dev zlib1g-dev liblzma-dev libpng12-dev tklib itcl3 itcl3-dev iwidgets4 itk3 itk3-dev build-essential libcdk5-dev libcurl4-gnutls-dev
sudo ln -s /usr/bin/make /usr/bin/gmake
5. Configure, Make and install the io_lib package
cd io_lib-1.12.5
./configure
make && sudo make install
6. Configure, Make and install staden
cd ../
cd staden-2.0.0bd-src
mkdir build.mavrick
cd build.mavrick
../configure
make && sudo make install
That is is. The staden package should now be installed.
One thing to note is that if you need samtools you will need to configure, build and make it prior to step 6 above
[1] Samtools is only needed by tg_index to build Gap5 databases from bam format files. Note that if used it must be built as a relocatable library by adding -fPIC to the CFLAGS in the samtools Makefile.
Thanks for the step by step guide. Was wondering about step 6 though, In which directory should the ‘build.mavrick’ directory be made?
Cheers
The build.maverick folder really can be created anywhere(actually you can even skip creating it and just run ./configure within the ~/staden folder), but the easiest place is to create it inside the ~/staden folder
I hope that helps. Let me know if you need any more help.
Worked out fine. Thanks
This is great. I got most of this to work for me until I got to step 6. With ../configure, I get an error as follows.
configure:2247: error: source directory already configured; run “make distclean”
there first
I tried typing make distclean in various directories within ~/staden without the error going away. Got this message instead
make: *** No rule to make target `distclean’. Stop.
Any ideas? I’m still a bit new to this.
I just updated the guide for step 6. I forgot the step where you change directory to the downloaded staden directory
Basically you have to execute step 6 within the extracted staden directory
My Fiance is a Microbiologist and struggles with compiling and understanding all of these applications so you are not alone in being new to all of this.
If you have questions or want help on other things feel free to ask. I actually enjoy creating guides for this stuff that helps others.
Hope that helps.
Thanks again. Unfortunately, I tried this and it didn’t work.
What happens is that in step 6, ../configure
(within ~/staden/staden-2.0.0b9.i686/build.mavrick)
gives
bash: ../configure: No such file or directory
One thing I noticed is that ~/staden/io_lib-1.12.5 has a file called configure, whereas there is no such file in ~/staden/stadent-2.0.09b.i686 or any of its subdirectories (including, no surprise, /build.mavrick) I’ve looked (but not exhaustively).
Should I try ../io_lib-1.12.5/configure from ~/staden/staden-2.0.0b9.i686/build.mavrick ??
Nevermind! I had wrong version of staden downloaded! The installation went – some error messages here and there…
Unfortunately, running gap4 from the directory caused the original terminal to crash. And with new terminal, I still cannot invoke any of the programs – gap4, gap5, etc. Oh well.
Try running gap4 from outside of the installation directory. After the instructions above it will be installed in /usr/local/bin so you can just type gap4 from the terminal in any directory and it will run.
I don’t actually know how to use the program so I don’t have any input files to test to see if my install crashes or not.
I finally found some time to work this through.
I got it to work on Fedora 16 first with help of their README.build file – your instruction made it easier to quickly decipher it. I then got it to work on Ubuntu 11.10, but it required a small re-write/rearrangements on a couple of MAKEFILE – this came via instructions posted at their forum.
http://sourceforge.net/projects/staden/forums/forum/347718/topic/4861055
Thanks again. The authors really should post installation instructions on their homepage AS WELL AS on the download packages – I should think this would not be so hard to do. Even with instructions, it’s plenty of work – quite overwhelming for a semi-informed newbie like me.