Deprecated - Toolforge no longer has a Grid, as of December 2023. These instructions are outdated. A future version of BWA that supports Toolforge concurrency will be forthcoming.

For Toolforge (as of August 2020)

1. After git clone https://github.com/greencardamom/BotWikiAwk ..

2. Add the following to .bash_profile of the Tool account (not your main login account)

export PATH=$PATH:/data/project/<toolname>/BotWikiAwk/bin

export AWKPATH=.:/data/project/<toolname>/BotWikiAwk/lib:/usr/share/awk

Replace "<toolname"> with the name of your tool (ie. the "become <toolname>" name). Log out and back in to take effect.

3. cd to ~/BotWikiAwk and tun ./setup.sh. Ignore warning if parallel is missing.

4. Add environment to crontab. Presumably one of your tools will eventually be running on the Grid via cron. The Grid inherits the environment from the crontab. Here is an example crontab for running a tool with BotWikiAwk

SHELL=/bin/bash
PATH=/sbin:/bin:/usr/sbin:/usr/local/bin:/usr/bin:/data/project/<toolname>/BotWikiAwk/bin
AWKPATH=.:/data/project/<toolname>/BotWikiAwk/lib
MAILTO=<email addr>
HOME=/data/project/<toolname>
LANG=en_US.UTF-8
LC_COLLATE=en_US.UTF-8

#              field          allowed values
#              -----          --------------
#              minute         0-59
#              hour           0-23
#              day of month   1-31
#              month          1-12 (or names, see below)
#              day of week    0-7 (0 or 7 is Sun, or use names)
#
37 5 * * 7 /usr/bin/qsub -e /data/project/botwikiawk/shorty/shorty.stderr -o /data/project/botwikiawk/shorty/shorty.stdout -V -wd /data/project/botwikiawk/shorty /data/project/botwikiawk/shorty/shorty.awk

Notice PATH and AWKPATH are updated with the BotWikiAwk paths. Also, when running a program with qsub use "-wd" (working directory) so it runs from the directory where the program is located.

5. Continue with normal setup instructions.