BIRCH/Bugs and fixes
From Bioinformatics.Org Wiki
- Cn3D only works on recent Linux-x86_84 machines. It doesn't work on the older Centos machines, nor on any of the Solaris machines. Almost certainly this is because libraries need to be updated in lib-xxx-xxx directories, because the older machines are using older libraries.
- Change format of BIRCH Administrator's email address so that it isn't a spam target.
- Replace heapsortHGL with a separate sort program
- Need better documentation for the fact that BIRCH changes the command prompt. Should we set an environment variable to let the user turn this off? This may be best to do in a $HOME/.birchrc file.
- Documentation pages could have an icon indicating whether a program or package is part of the BIRCH core or locally-installed.
- For local.cshrc.source and local.profile.source: option for shell to recognize BACKSPACE key.
- On some systems, mv is aliased to mv -i. This will cause some scripts to fail if they try to overwrite an already existing file, because the script will try to prompt the user. The problem has been fixed in dnadist.csh and protdist.csh, but other scripts, and the .GDEmenus files, need to be checked to see which ones might be susceptible to this problem.
- get programs to recognize new amino acid symbols: J = Leu/Ile = Xle; O = Pyl = pyrrolysine. In particular, the following programs packages need to be looked at:
- GNOME, KDE menus
- rethink strategy for local copies of PIR/SwissProt
- add newuser and nobirch to birchdb (write man pages)
- miniBIRCH: let's see if we can shrink the size of the .tar.gz file by reorganization of $doc or $dat directories.
- complete set of pattern discovery/pattern matching programs
- better support for genomic sequences of arbitrary length
- need a more sophisticated usage logging mechanism
- $BIRCH_TMP points to a directory that can be used by scripts for temporary files, usually /usr/local/tmp. We probably need a standalone script that can be called by other scripts to see if this directory is available, and if so, to use it.
- It probably isn't hard to add code that would let each user have their own cshrc.source or profile.source files that could override the local BIRCH system. But, it there any advantage to doing this, versus just telling them to modify .cshrc or .profile?