anyone know how to get the debian Med tools?

[coolgenes]

I was looking at Bio-Linux and was able to successfully apt-get some of those pachages (don't get the handlebar, it hangs). But found that the Debian MedTools holds a lot of molecular type tools I could use but am having trouble gaining access to them. I contacted the tools moderator but no reply. Also, if anyone has any success getting Samtools and Staden to install on Ubuntu please let me know.

[coolgenes]

bump?

[Chronon]

Sorry, I don't have any special info, but if package versions for dependencies are not consistent between Debian and Ubuntu then you could consider trying to build these tools from source.

[ajt]

I was looking at Bio-Linux and was able to successfully apt-get some of those pachages (don't get the handlebar, it hangs). But found that the Debian MedTools holds a lot of molecular type tools I could use but am having trouble gaining access to them. I contacted the tools moderator but no reply. Also, if anyone has any success getting Samtools and Staden to install on Ubuntu please let me know.

Hello, coolgenes.

Bio-Linux 5.0 is based on Ubuntu 8.04 LTS, and there are some 'hardy' dependencies. Have you tried installing the Bio-Linux Staden?


# add to /etc/apt/sources.list:
# deb http://nebc.nox.ac.uk/bio-linux/ unstable bio-linux

aptitude install bio-linux-staden


Bye,

Tony.

[coolgenes]

Thanks AJT, yes I've tried that. the problem with the BioLinux lib is that they aren't up to date. both the PhredPhrap and the Staden are out of date enough I think I have to install them myself, I just don't think they have enough help there to continue to compile all the updates to the molecular and evolution type analysis programs. I was hoping the Med tools would be better or at least compliment what BioLinux has

[parktownprawn]

The debian med packages are in Ubuntu since Ubuntu is derived from Debian


Try typing sudo apt-get install med-bio.

If you want to see what packages are available check out

http://debian-med.alioth.debian.org/tasks/bio

To see what Debian med packages there are in Ubuntu try typing

apt-cache search med-

I have no idea how up to date these are.