The latest build of the Staden Package has been released. The changes are primarily incremental, with a few new graphical plots and text outputs for searching for sequence variations (whether they be SNPs or misassemblies). Naturally several bugs have also been removed (and hopefully fewer added).
This version also includes the first Microsoft Windows release since May 2003, so windows users may want to check the release notes for the 1.4.0 version too.
For full release notes, see the 1.5.3 release notes page.
For downloads, please visit the SourceForge files section.
Thanks to staff at Imperial College Bioinformatics Centre for providing us with precompiled Solaris binaries for the v1.4 release.
More information on this can be found at https://sourceforge.net/forum/forum.php?forum_id=370196.
Firstly, to keep administration of CVS version numbers easy (and to move away from having a date in the release which is always problematic when testing new releases spanning the new year) I have renumbered the version numbers. From this point on expect v1.4, 1.5, and so on.
Secondly, the source code and binaries for the new 1.4 are now available for SOME platforms. I hope to expand this list soon, but currently I do not have the tools or hardware available to build a MS Windows release. If you wish to undertake this build, feel free to do so (but contact me first please so I can coordinate efforts if more than one person is trying this).
Binaries are currently available for Linux, Alpha and MacOSX from the SourceForge download page.
Full release notes are available here.
The CVS tree for the package source code has now been uploaded and installed on SourceForge. Thanks to the SF team for doing this. It can be browsed by going here.
The MRC have released the soruce code for the Staden Package under a BSD-style licence. Subsequently I (James Bonfield) have created a SourceForge project and are in the process of copying over the prebuilt binaries and the last source tree at the time the group disbanded.
The SourceForge project home directory is https://sourceforge.net/projects/staden.
Since I moved to the Wellcome Trust Sanger Institute I have been supporting Gap4 and the Prefinishing code locally. This has included making numerous additions to Gap4. Once local consent has been granted I plan to upload the CVS tree to SourceForge and to build new source tarballs, and binaries for several systems (Linux and Alpha for sure, but others are doubtful at present).
It is important to realise that the WTSI, MRC, or me personally have no obligation to support the users or the source code. Being pragmatic though it is likely that modifications made within WTSI will be of use to the wider community and vice versa, so "support" for Gap4 and Prefinish is likely to exist in a reduced form. I do not have the time to keep tools that are not used locally up to date. This includes Pregap4 and Spin. Please contact me if you feel you can help in this area.
So to continue this project needs support from you all (ie the users). To this end I would encourage use of the SourceForge forums or the newsgroup.