Add CL option to specify queue name in Grid Engine
Use env perl in shebangs for portability
Add verbose mode, like dry_run but does execute
Add h_vmem memory allocation either by CL arg or module.
‘h_vmem’ instead of ‘vf’ option can be chosen for all qsubbed commands using the -h_vmem CL option or hardcoded into the wrapper modules by making them return ‘h_vmem’ as a prefix to their memory demand, e.g:

if($required_mem){
	print 'h_vmem'.CF::Helpers::allocate_memory($required_mem, ‘5G', ‘20G');
	exit;
}
Fixed bug in add genome dialogue
Bug: Bowtie2 path didn’t go in unless accompanied by a Bowtie1 path in same dialogue
trim_galore: fix to eliminate warning on non-numerical “==“
Fixed 2 bugs in bowtie2.cfmod bowtie2 path selection
Bug 1: bowtie2 path was never accepted unless bowtie1 path existed
Bug 2: bowtie2 path was never replaced with bowtie1 path in the case where bowtie1 path exists but bowtie2 path doesn’t
Give more info to cfmods to decide memory and cores requirements.

In cf, decide cores and memory only after determining prev_job etc. More parameters now fed to —-mem and —-cores decision process so that more memory can be requested for bigger files and can be controlled in pipeline file.
e.g. in .cfmod, to pass h_vmem request from pipeline arg “h_vmem”:
if($required_mem){
	my @h_vmem = ("");
	my ($files, $runfile, $job_id, $prev_job_id, $cores, $mem, $parameters, $config_ref) = CF::Helpers::load_runfile_params(@ARGV);
	@h_vmem = grep(/^h_vmem$/, @$parameters);
	print $h_vmem[0].CF::Helpers::allocate_memory($required_mem, '8G', ‘80G');
	exit;
}
Disable bowtie2->1 defaulting as it doesn’t work
Merge pull request #11 from stu2/geopts

Geopts - additions from @stu2 for better GRIDEngine support (h_vmem as well as vf, queue names) and better script portability. New verbose feature. Some bowtie2 path bug fixes.
Changed tophat cleanup fn from _accepted_hits.bam to _tophat.bam
Added STAR genomes to hard-coded genome types
Add env perl to shebangs for helper modules
Fix bug in available memory offer in most cfmods

Bug: Available memory offered by core cf was being interpreted as only 1 byte because it was logical not string in getopts
New runfile parser for use in pre-run memory allocation in cfmods
Now cfmods are given the runfile, genome, #cores and @parameters to decide on memory and cores. They can parse the runfile with CF::Helpers::parse_runfile_prerun and the rest as shown in example_module commented-out section.
Trim_galore cfmod can now parse the -q argument from pipeline
Add a wrapper for STAR aligner
Tidy up sub parse_runfile_prerun
Add samtools module to sort sam / bam files
Add samtools module to sort sam / bam files