Merge pull request #37 from CraigPorter/master

Added list_species_sequenced.pl to pathdev bin.
Added run_jscript to production
Change to jspecies from jscript
rename assembly_stats script
Merge pull request #38 from andrewjpage/master

assembly stats
add convert_gff3_to_gff2.pl
Merge pull request #39 from andrewjpage/master

convert_gff3_to_gff2.pl
added chado_dump_introns
Merge remote-tracking branch 'upstream/master'
Merge pull request #40 from tcarver/master

added chado_dump_introns 
Added cshrc to bash perl script
merge rna seq
Merge pull request #41 from andrewjpage/master

merge rnaseq
fastq to fasta
Merge pull request #42 from andrewjpage/master

fastq to fasta