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Staden Package version 2.0 beta test

I'm pleased to announce the first beta-test release of what will become version 2.0 of the Staden Package.

In the last few releases Gap5 has been releases as a separate package with it's own directory layout. In version 2.0 I plan for the Staden Package to be integrated as a whole again, with a single package containing gap4, gap5, spin, etc.

The other major change in 2.0 vs 1.x releases is the directory layout and source building has had a large overhaul. The code should be vastly easier to build than the old crufty release, and to encourage testing for the first beta test I'm only releasing source.

For ease of maintenance the documentation and source have been split into two packages, as the result of "building" the documentation is not platform specifc. It is however a required component of any binary distributions as the documentation also serves for the inbuilt help for the programs.

The third-party package files (itcl, itk, incr widgets, etc) and the use of Makefile.thirdparty no longer exists. Instead you should use the various --with-itcl=DIR type parameters when building. As an example I recently built the code (along with samtools for tg_index) on a fresh server install of Ubuntu 9. I made the following notes during building. (See end)

Finally, the RSS feed may not be updating correctly, so direct links to the downloads are:

https://sourceforge.net/projects/staden/files/staden/2.0.0b1/staden-2.0.0b1-src.tar.gz/download
https://sourceforge.net/projects/staden/files/staden/2.0.0b1/staden_doc-2.0.0b1-src.tar.gz/download
https://sourceforge.net/projects/staden/files/io_lib/1.12.1/io_lib-1.12.1.tar.gz/download

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Dependencies to build io_lib, staden and staden_doc

Ubuntu

Ubuntu 9 via minimal server at http://www.thoughtpolice.co.uk/vmware/

(apt-get install openssh-server)

io_lib-1.12.1
-------------

apt-get install gcc
apt-get install make
apt-get install zlib1g-dev
apt-get install libcurl4-dev

./configure --prefix=/usr/local/staden
make
make install

samtools-0.1.5c
---------------

apt-get install ncurses-dev

make

# There's no "make install" target with this samtools release, but
# either copy the bits you want somewhere manually or just leave in
# situ as the staden compilation can be pointed at this directory.

staden-2.0-src
--------------

apt-get install itcl3-dev
apt-get install itk3-dev
apt-get install iwidgets4
apt-get install tklib
apt-get install libpng-dev
apt-get install xutils-dev ;#makedepend
apt-get install g++

# This isn't necessary if we install somewhere in our default path.
# (Alternatively face the pain and reenable rpath for io_lib, but
# it'll probably bite you at some stage if you're doing code
# development.)
export LD_LIBRARY_PATH=/usr/local/staden/lib

./configure --prefix=/usr/local/staden \ --with-iolib=/usr/local/staden \ --with-samtools=`pwd`/../samtools-0.1.5c

staden-doc-2.0-src
------------------

apt-get install tetex-bin
apt-get install imagemagick
apt-get install m4
apt-get install texinfo

make unix
make install PREFIX=/usr/local/staden

Posted by James Bonfield 2009-08-07