About BIRCH

• Which hardware/software platforms does BIRCH run on?
• 
  

Installation and Updating

• Installation of the FASTA programs fails
  
• I can run programs from my BIRCH administrator's account, but not from any other account
• After I ran 'newuser', my prompt changed. I like my prompt. How can I stop BIRCH from changing it?
  

Adding 3rd party programs or documentation to my BIRCH site

Troubleshooting

• Lots of things don't work. I keep seeing 'NoClassDefFoundError' messages
• bioLegato works, but for many of the programs that I try to launch (eg. NUMSEQ, fasta, NCBI BLAST) I get bash: numseq : command not found
  
• GDE will not launch, and gives Xview error messages indicating missing fonts
• On Solaris10, when I try to create a tar file or open a tar file, I get a 0 length tar file and also a 0 length file called @LongLink. However, the same file gives me no problem on Linux. What's up?
  

Design considerations

• Why is customdoc.py needed? Couldn't you use server-side includes to accomplish the same thing?
• Why are many of the BIRCH scripts written for csh, rather than sh? In particular, bash is more powerful than csh.
  

About BIRCH

• Which hardware/software platforms does BIRCH run on? I'll try to answer this in the form of a chart:
  

  OS	Hardware	BIRCH nomenclature	Comments
  Solaris	Sparc 64	solaris-sparc	Compiles and runs
  	Sparc 32		some older apps were compiled on this platform, but others were not. BIRCH has never been tested on 32-bit Sparc machines
  	AMD64 (x64)	solaris-amd64	Compiles and runs. Most apps compiled on this platform, but a few older programs were compiled on 32-bit i86 machines.
  	32-bit Intel (x86)		This is an obsolete platform. Only a few of the BIRCH apps mentioned above would run here. BIRCH has never been tested here.
  Linux (Fedora, Gentoo, Ubuntu 32-bit)	32-bit Intel (x86)	linux-intel	compiles and runs
  	64-bit Intel or AMD		32-bit binaries work correctly on 64-bit architecture running 32-bit Linux.
  Linux (64-bit)	Sparc 64		not tested.
  Linux (64-bit)	64-bit Intel, or AMD	linux-x86_64	Compiles and runs. Thoroughly tested.
  MacOSX	64-bit Intel	osx-x86_64	Compiles and runs. Thoroughly tested.

Installation and Updating

• Installation of the FASTA programs fails - The most common cause of this error is that some systems do not allow you to connect to an outside system by annonymous FTP. In this case, the fasta install scripts in install-birch/fasta are trying to connect to ftp.virginia.edu as user 'anonymous'. If your system does not allow anonymous FTP downloads, contact your Unix system administrator for help. Once you get FTP working, you can run these install scripts from the command line, rather than re-doing the entire BIRCH install.
  
• I can run programs from my BIRCH administrator's account, but not from any other account - Remember, each user must run the newuser script to set up their accounts to use BIRCH. See the First Time Setup page in the 'NEW USERS' box on the BIRCH web site.
• After I ran 'newuser', my prompt changed. I like my prompt. How can I stop BIRCH from changing it? The command line prompt is set in $BIRCH/local/admin/local.cshrc.source for C-shells (csh, tcsh) and in $BIRCH/local/admin/local.profile.source for Bourne-like shells (eg. bash, sh, etc.). Simply comment out the lines that set the prompt, and users will revert back to the system prompt.
  

Adding 3rd party programs or documentation to my BIRCH site

Troubleshooting

• Lots of things don't work. I keep seeing 'NoClassDefFoundError' messages - It is likely that Java is not set up correctly on your system. See inst.java.html.
• bioLegato works, but for many of the programs that I try to launch (eg. NUMSEQ, fasta, NCBI BLAST) I get bash: numseq : command not found - This is almost certainly because the wrong platform was set when BIRCH was installed. Java programs such as bioLegato work because they run through the Java interpreter. Compiled programs won't work, because BIRCH is looking in the wrong directory for binaries. For example,  if you had installed the 64-bit Linux binaries (linux-x86_64) but chosen "linux-intel" as the platform when you first ran birchconfig. If that is true, "echo $BIRCH_PLATFORM" would print "linux-intel". 
  
  The following steps will fix this problem:
  
  1. In $BIRCH/local/admin/BIRCH.properties, change BirchProps.platform to the correct platform eg. linux-x86_64.
  2. In $BIRCH/local/admin/platform.profile.source, comment out the line that says 'BIRCH_PLATFORM=linux-intel' and uncomment the line that says 'BIRCH_PLATFORM=linux_x86_64'.
  3. In $BIRCH/local/admin/platform.source, comment out the line that says 'setenv BIRCH_PLATFORM linux-intel' and uncomment the line that says 'setenv BIRCH_PLATFORM linux_x86_64'.
  
   
  
  
• GDE will not launch, and gives Xview error messages indicating missing fonts - Messages indicating missing fonts have been seen on some installations of Gentoo and Centos:
  

  XView warning: Cannot load font
  '-b&h-lucida-medium-r-*-*-*-120-*-*-*-*-*-*' (Font package)
  XView warning: Cannot load font
  '-b&h-lucida-medium-r-normal-sans-*-120-*-*-*-*-*-*' (Font package)
  XView error: Cannot open connection to window server: :0.0 (Server package)

  The problem has been fixed as follows: The required fonts from  were added to lib-linux-intel and lib-linux-x86_64 in a directory called gde.fonts. The following scripts were changes to add these fonts to the fontpath: dgde, gde, mgde, tgde and treetool.
  
  Note: The only fonts included in gde.fonts were the fonts necessary to make gde and treetool work. If you still get these messages try installing fonts-xorg-6.8.2, available your Linux distribution. Please send me a message at psgendb@cc.umanitoba.ca and let me know what messages you got, and whether or not this fix worked.
• On Solaris10, when I try to create a tar file or open a tar file, I get a 0 length tar file and also a 0 length file called @LongLink. However, the same file gives me no problem on Linux. What's up? - On Solaris10, tar can't handle very long filenames. So somewhere in the directory tree for the directory you are trying to archive is one or more files with long names. Tar works on Linux because Linux uses GNU tar. GNU tar is also available on Solaris as 'gtar'. So use 'gtar' for working with archives with long filenames. See http://openacs.org/forums/message-view?id=394174.

Troubleshooting

• Why is customdoc.py needed? Couldn't you use server-side includes to accomplish the same thing? - The short answer is that at the Univ. of Manitoba, personal web pages are not permitted to utilize .htaccess files, which are necessary for SSI. If it's not allowed here, chances are it won't be allowed at other places.
  
• Why are many of the BIRCH scripts written for csh, rather than sh? In particular, bash is more powerful than csh. - In recent years, the Bourne family of shells, particularly bash, has been winning mind-share from the C-shell family (eg. tcsh, csh). BIRCH was begun at a time when csh shells were quite commonly used. As well, there many reasons why csh syntax is a bit more programmer friendly than sh syntax. Nonethless, on many platforms today csh may not even exist in a default configuration, or may not be adequately supported by sysadmins. Therefore, we are in the process of converting all csh scripts to sh scripts. This is a job that can only be semi-automated and requires that every csh script be at least partly recoded by hand. Therefore, conversion is running in 2 phases: 1) convert all install scripts (done)  2) convert all other scripts. (in progress) The latter will probably happen over many releases. So in the mean time, csh is still needed.
  
  In any event, we probably need to support csh/tcsh for the forseeable future, because many users will still use these shells.