substitute paths written into macros

[westram]

Motivation:

• macros should be exchangeable between accounts (etc.)

Problem:

• paths written into macros cause failure, if executed
  • in different accounts
  • with different arb-versions (if multiple versions installed on one machine)

Possible solution:

• define a set of environment variables that should act as directory-variables, e.g.
  • ARBHOME
  • ARB_PROPS
  • ARB_WORKDIR
  • HOME
• when writing a string into a macro, substitute directories occurring in string by environment-read (e.g. '/home/ralf/examples/xxx.fasta' ⇒ $ENV{HOME}.'examples/xxx.fasta')

Possible place for substitution: write_as_perl_string()

Please note that these environment variables do not need to be explicitely defined, even if undefined arb uses a default value for them! To make the substitution work, ARB needs to export these variables to the environment before calling the macro!

[westram]

• calling submacros uses relative paths since [11791]