Would be nice if run0.{sh,bat} could use variables.

[SimonGreenhill]

e.g. instead of multiple lines of this:

cp /tmp/analysis/step0/beast.xml.state /tmp/analysis/step1
cd "/tmp/analysis/step1"
java -cp "/Applications/Phylogenetics/BEAST 2.4.0/BEAUti.app/Contents/Java/Classes:/Applications/Phylogenetics/BEAST 2.4.0/BEAUti.app/Contents/Java/launcher.jar:/Users/simon/Library/Application Support/BEAST/2.4/BEAST/lib/beast.jar:/Users/simon/Library/Application Support/BEAST/2.4/BEAST/lib/beast.src.jar:/Applications/Phylogenetics/BEAST 2.4.0/lib/beast.src.jar:/Users/simon/Library/Application Support/BEAST/2.4/Babel/lib/Babel.addon.jar:/Users/simon/Library/Application Support/BEAST/2.4/Babel/lib/itextpdf-5.5.9.jar:/Users/simon/Library/Application Support/BEAST/2.4/BDSKY/lib/BDSSM.addon.jar:/Users/simon/Library/Application Support/BEAST/2.4/BEAST_CLASSIC/lib/BEAST_CLASSIC.addon.jar:/Users/simon/Library/Application Support/BEAST/2.4/BEAST_CLASSIC/lib/mtj.jar:/Users/simon/Library/Application Support/BEAST/2.4/BEASTLabs/lib/BEASTlabs.addon.jar:/Users/simon/Library/Application Support/BEAST/2.4/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/Users/simon/Library/Application Support/BEAST/2.4/morph-models/lib/MM.addon.jar:/Users/simon/Library/Application Support/BEAST/2.4/subst-bma/lib/SubstBMA.addon.jar:/Applications/Phylogenetics/BEAST 2.4.0/lib/beast.src.jar:/Users/simon/Library/Application Support/BEAST/2.4/BEAST/lib/beast.src.jar" beast.app.beastapp.BeastMain -resume -java -seed 815032149 beast.xml

could become:

SEED=815032149
CWD="/tmp/analysis/"
CLASSPATH="/Applications/Phylogenetics/BEAST ....etc"

cp $(CWD)step0/beast.xml.state $(CWD)step1
cd "$(CWD)step1"
java -cp $(CLASSPATH) beast.app.beastapp.BeastMain -resume -java -seed $(SEED) beast.xml

...which would then make the subsequent analysis scripts easier to move between machines (say from laptop to a cluster, where e.g. CWD and CLASSPATH is different).

Not sure how .bat files handle variables though, so this might be tricky to get working cross-platform.

Even better would be a loop, as then you could just increment $MAX_STEPS and rerun, but again cross-platform compatibility could be nightmare (e.g. from memory for loop syntax isn't consistent even across POSIX).