BIRCH - Special considerations for packages

Rationale: Bioinformatics software ranges from a single program distributed as a standalone binary to a large package of dozens of programs, with many documentation files and datafiles. In many cases, an application assumes that all of these files are organized in a single hierarchical directory, and it is not practical to simply move them to the BIRCH bin, $doc and $dat directories. The following example illustrates some of the salient points about installing packages:

Where to install the files

Example: Staden Package

The Staden package should be installed in a directory such as staden-1.5.3, indicating the version number, with a symbolic link named 'staden'. The documentation and data directories are pointed to by symbolic links from the $local/doc and $local/dat directories, respectively. The staden symbolic link should be the only link that needs to be changed when the package is upgraded to a new version.

The Staden package is unusual in that it has login scripts: login.source and profile.source. These scripts set the $STADENROOT environment variable as the location of the Staden package, as well as other variables that are built from $STADENROOT. Although the Staden documentation recommends that one of these scripts be run at login time, the scripts set the $LD_LIBRARY_PATH, which could interfere with getting other programs to run. The safest alternative is to run each application from a wrapper script that calls staden.login or staden.profile. $BIRCH/script contains wraper scripts called pregap4, gap4, spin and trev that run the Staden binaries of the same names. Consequently, if you install Staden locally, these scripts will automatically run these programs correctly.

$local/pkg

$local/doc

staden-->../pkg/staden/doc

$local/dat

staden-->../pkg/staden/userdata

How to find the binaries

For most packages, there are two straightforward ways to make it possible for BIRCH to find the binaries.

move the binaries to $local/bin-xxx-xxx directories - This is accomplished using a single command, such as 'mv * $local/bin-solaris-sparc' or 'mv * $local/bin-linux-intel'. It has the disadvantage that there is no easy way to know the version of a program, without running it.
make symbolic links from the $local/bin-xxx-xxx directories to the bin directory for the package - This has the advantage that the links shouldn't break, when the package is updated.

Please send suggestions of comments regarding this page to psgendb@cc.umanitoba.ca