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A tiny package manager for crucial unix and bioinformatics tools
This project forked from drio/bio.brew
A tiny package manager for crucial unix and bioinformatics tools
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 :
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...
Now what would be even nicer is if module files were automagically generated as well...
something like link_from_stage for lib / lib64
many of the current recipes are created for the old version of bio-brew. need to check and correct existing recipes
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.
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
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
something like link_from_stage for man pages
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