Slight confusion in example scripts, and sga-align not getting installed

[vuw-ecs-kevin]

I'm merely the installer of SGA on a shared HPC resource, but I wanted to say thanks for providing some examples so that an installation can be tested out, ahead of passing it over for use by the bioinformaticians, however , I did get a little confused.

The sga-celegans.sh script hard-wires a version (now old) of the main SGA binary in a variable, SGA_BIN, which is the used throughout the script, vis:

# Parameters
SGA_BIN=sga-0.9.31

however a make install doesn't see a versioned-binary installed, just a bare sga.

Later on in the script, there's a couple of hardcoded references to paths to other SGA scripts, with non-versioned names, that SGS does install (though see below).

# Realign reads to the contigs
~/work/devel/sga/src/bin/sga-align --name celegans.pe $CTGS $IN1 $IN2

# Make contig-contig distance estimates
~/work/devel/sga/src/bin/sga-bam2de.pl -n $MIN_PAIRS --prefix libPE celegans.pe.bam

# Make contig copy number estimates
~/work/devel/sga/src/bin/sga-astat.py -m $MIN_LENGTH celegans.pe.refsort.bam > libPE.astat

I note that in the sga-ecoli-miseq.sh script, everything, including the scripts above, has been turned into a variable

SGA_BIN=sga
BWA_BIN=bwa
SAMTOOLS_BIN=samtools
BAM2DE_BIN=sga-bam2de.pl
...

so I wondered if you might update the sga-celegans.sh script in a similar manner.

Having resolved that confusion, I then noticed that the make install I had done, had only placed these four files

sga  sga-astat.py  sga-bam2de.pl  sga-mergeDriver.pl

into the bin directory and not copied over the sga-align script that the sga-celegans.sh example script refers to, indeed there are a number of scripts in the source distribution's src/bin directory that are not installed by a make install from the src dir.

Apologies if I have missed something obvious. I am working with a 0.10.14 tarball.