Makefile: Fixed paths to mappings dir for new scripts dir location

Renamed util to bin

Moved inputs_Makefile to inputs/input.Makefile

Moved bien_password to new config dir

Moved sample inputs to test dir

Added symlink from scripts to new scripts destination

Removed now-empty scripts dir

Moved everything in scripts to root. inputs_Makefile: Don't run "all" when installing.

Renamed bien_map to map

Moved map to util

fix_permissions: Don't chmod symlinks

inputs_Makefile: Auto-generate map to VegBIEN and import data into vegbien from input DB

inputs/SALVIAS: maps to VegX and VegBIEN

bien_map: Runs map with BIEN defaults

join_sort: Sorts a join on the output col

inputs_Makefile: Require dbEngine var instead of defaulting to MySQL

Moved inputs into svn

Moved pre-BIEN 3 files into _archive folder

test/map: Use db.sh syntax in *.sh tests

inputs_Makefile: Generate db.sh with DB access info

inputs_Makefile: Changed GRANT ALL to GRANT SELECT. Added REVOKE ALL. Added $(db).sql as prerequisite of install in case it needs to be auto-generated.

scripts/Makefile: Added action for postgres-Darwin target

scripts/Makefile: Added postgresql to postgres-Linux apt-get packages

test/map: Changed to work on both nimoy and vegbiendev by selecting the appropriate MySQL user and password

env_password: Added optional message arg

Added uninstallation of inputs to Makefiles

scripts/Makefile: Create bien user w/o prompting for password. Fixed syntax error.

scripts/Makefile: Fixed syntax error

Inputs now include inputs_Makefile to get mysql command, etc.

scripts/Makefile: Use bien MySQL user for installing inputs

scripts/Makefile: Use root MySQL user for creating bien user

scripts/Makefile: Don't use root as MySQL admin user. Removed no-longer-needed sub-makes for setting DB login vars.

Changed vegbien_dest and users of it to use separate bien_password file

fix_permissions: Extend all user permissions to group

scripts/Makefile: Added inputs

mappings/Makefile: Cleaned up

fix_permissions: Don't add group write perms to read-only files

scripts/Makefile: Made read command syntax compatible with /bin/sh

scripts/Makefile: Ignore errors about missing packages

scripts/Makefile: Fixed escape character for /bin/sh

scripts/Makefile: Added dependency installation. Makefiles: Use _not_file instead of FORCE for clarity. Use $(os) var

fix_permissions: Configured output verbosity

Added fix_permissions to set correct permissions on shared bien files

Removed VegBank scripts which are no longer needed

Removed VegBank scripts which are no longer needed

Renamed vegbien_dest.sh to vegbien_dest to reflect that it is also includable by Makefiles

DB user creation: Clarified instructions

scripts/Makefile includes vegbien_dest.sh directly

Moved db user creation to scripts/Makefile. Removed now-unneeded admin scripts.

Removed VegBank scripts which are no longer needed

scripts/Makefile: Added empty_db target which uses vegbien_empty.sql

mappings/Makefile: Fixed bug where var containing prerequisistes needed to be defined before used. Added support for different sed flags to use extended regular expressions.

Added auto-generated vegbien_empty.sql to empty the vegbien db

Test output to VegBIEN instead of VegBank

VegX-VegBIEN.organisms.csv: sort output of repl

review: Added nullglob

review: Don't process replacements spreadsheets

Moved schema replacements from VegBank-VegBIEN.csv to VegBank-VegBIEN.schema.csv

VegBank-VegBIEN.csv: Support PostgreSQL before 8.4

repl: Added support for blank lines. Only add whole word regexp code to inputs w/o any regexp metachars.

Create vegbien db from mappings/schemas/vegbien.sql

VegBank-VegBIEN.csv: Added replacements for SQL create script conversion

Generate vegbien db create SQL from vegbank.sql using repl

Generate vegbien db create SQL from vegbank.sql using repl

repl: Fixed bug in reading arguments

repl: Don't add whole-word regexp for inputs that already have regexp metachars

Removed mappings/VegBank-VegBIEN.organisms.csv because now using replacements spreadsheet

mappings: Generate mappings to VegBIEN using VegBank-VegBIEN.cs replacements spreadsheet

mappings: Generate mappings to VegBIEN using VegBank-VegBIEN.cs replacements spreadsheet

mappings: Generate mappings to VegBIEN using VegBank-VegBIEN.cs replacements spreadsheet

Added repl to perform replacements on a spreadsheet or file

scripts/Makefile: removed extra test-% target

README.TXT: Updated

scripts/Makefile: install/uninstall targets

bien_user_create: Print instructions in sequence with password prompts

mappings to VegBIEN: Accounted for remaining ALTER TABLE statements

Renamed format*_for_review to review and added for_review to make clean

mappings: Added mappings to VegBIEN

mappings/Makefile: Simplified

mappings/Makefile: Simplified

README.TXT: Updated

Added vegbien DB admin scripts

join_all_vegbank: Sort output by both columns

mappings/VegX-VegBank.organisms.csv: Sorted by both columns

mappings/Makefile: Sort VegBank-VegBIEN.organisms.csv by both columns

extract_plot_map: Removed because functionality now in Makefile

sort: Can sort on multiple columns

Added basic VegX-VegBIEN mapping

Added union and join_passthru

env_password: Print Usage message to stderr

test/map: Create output dir if it doesn't exist

Converted scripts back to bash that required bash-specific features

Converted scripts back to bash that required bash-specific features

Fixed test/map to work with sh

Replaced /bin/bash with /bin/sh

join: Added usage item for repeated joins

join: Changed order of args and redirects to be more intuitive

Renamed ch_map_root to ch_root

Renamed join_maps to join

Merged test Makefile into main scripts Makefile