vlandham / bio.brew Goto Github PK

something like link_from_stage for man pages

many of the current recipes are created for the old version of bio-brew. need to check and correct existing recipes

Currently, bb list shows all recipes and then indicates for each if it is installed, activated or faked.

Should add bb list installed that displays only installed tools

lib/common.sh contains a number of global variables that should be scoped a bit better to avoid naming collisions with existing variables.

example: BIN_DIR

could be BB_BIN_DIR or BBREW_BIN_DIR

Now what would be even nicer is if module files were automagically generated as well...

• http://www.hpc.cam.ac.uk/user/modules.html#modules
• https://github.com/ucr-bioinformatics/biocluster-modules/tree/master/main

Currently multiple versions of a tool are supported primarily by modifying the $STAGE_DIR and $LOG_DIR to include the $recipe.

This works, but seems a bit fragile.

It is also confusing as these global variables are redefined in bin/bb after being defined in lib/common.sh

This should be improved. No ideas on how to do this yet...

homebrew has a feature where you can define a patch and apply it to a source file (like a Makefile) during the install.

We need to replicate something like this for installs that require changes to the source.

something like link_from_stage for lib / lib64

Looks like bb list doesn't sort based on version number or active/installed:

picard : 
I : picard_1.62              :  java
A : picard_1.65              :  java
- : pv-1.1.4                 :  
- : R-2.12.0                 :