binaries required by mktree.sh are unavailable

[koadman]

The mktree.sh script in the simulation pipeline reconstructs a phylogeny of the simulated genomes via progressiveMauve genome alignment. the various programs used by this script are not present or documented. I believe this is an optional step, simply a sanity check on sgEvolver. If so, is it ok to remove this target from SConstruct_evo.py?

[cerebis]

I don't want to entirely remove validation steps. You will probably find other things that fall into this same category.

I can see the argument for a debug mode.

[koadman]

I guess this is just one example of the bigger issue of dependencies. grepping out $HOME showed me the following (probably not exhaustive) list of 3rd party binaries that might be needed:

pbsrun_ART.sh:ARTEXE=$HOME/bin/ART/art_illumina
pbsrun_BAMFILTER.sh:SAMTOOLS=$HOME/bin/samtools
pbsrun_BWA.sh:#BWAEXE=$HOME/bin/bwa-0.7.6a/bwa
pbsrun_HiC.sh:HICEXE=$HOME/git/proxigenomics/simulation/hic_simulator/src/simForward.py
pbsrun_INDEX.sh:BWA=$HOME/bin/bwa-0.7.6a/bwa
pbsrun_LAP.sh:export BT2_HOME=$HOME/software/bowtie2-2.2.2/
pbsrun_LAP.sh:LAP_CALC=$HOME/git/lap_release_1.1/aligner/calc_prob.py
pbsrun_LAST.sh:LASTAL=$HOME/bin/lastal
pbsrun_LAST.sh:LASTDB=$HOME/bin/lastdb
pbsrun_LAST.sh:MAFCONV=$HOME/bin/maf-convert.py
pbsrun_MAP2.sh:BWAEXE=$HOME/bin/bwa-0.7.6a/bwa
pbsrun_MAP.sh:BWAEXE=$HOME/bin/bwa-0.7.6a/bwa
pbsrun_MAP.sh:SAMTOOLS=$HOME/bin/samtools
pbsrun_METAART.sh:MA_PATH=$HOME/git/proxigenomics/simulation/hic_simulator/src/metaART.py
pbsrun_METAART.sh:ART_PATH=$HOME/bin/ART/art_illumina
pbsrun_MINIA.sh:MINIA=$HOME/bin/minia-1.6088/minia
pbsrun_RMCL.sh:CMD=$HOME/bin/rmcl
sge_a5submit.sh:export ITHREE_GIT=$HOME/git/ithree
sgerun_LAP.sh:LAP_CALC=$HOME/git/lap_release_1.1/aligner/calc_prob.py
sgerun_LAPSUM.sh:LAP_SUM=$HOME/git/lap_release_1.1/aligner/sum_prob.py
sgerun_METAART.sh:MA_PATH=$HOME/git/proxigenomics/simulation/hic_simulator/src/metaART.py

What is the right way to tackle the issue? Options that come to mind include putting static linux binaries into github (licensing permitting), building a redistributable VM, or (gasp!) Docker. Documenting all the dependencies and telling users to install them would be yet another solution (though doesn't do much to help get people started quickly).