Merge pull request #1 from eastmallingresearch/master

Pull request to adarmitage github account
path_pipe.sh is being developed as a stand alone shell script that does not call on any other shell scripts. It still calls on other .pl tools.
path_pipe.sh continued development with parrallelistion removed. Parallelisation returned to parallel_signalp.sh and submit_signalp.sh. mimp finder modified to establish why not printing to file - possibly due to unecessary chomp.
path_pipe.sh pipeline complete. Ready for error checking. Restored parrallel_signalp.sh to original functionality
modified how collects data from input files. Now takes fields from the end of the string. These are collected using cut after a reverse.
Corrected output file names beginning with $all.* to $STRAIN. This will ease later identification of which file belongs to which analysis.
copy step in line 29 now uses stored variable
modified how program opens input file
corrected typo in my
changed how sets variables for organism and strain and sorted contigs file. Now searches from the end of the directory chain and is now specific to the output from assembly_pipe.sh
Added echo to ensure that files are present in the temporary directory
Corrected typo
changed print_atg.pl input from file in local directory to full file path to correct error where not recognising []
corrected error in print_atg.pl where input files were being counted from [] rather than []
corrected missing strain name from .aa.cat.fa
removed  from around * when performing cp as it prevents expansion of *. THis was preventing outfules to be copied properly.
A script to submit all assemblies present in the directory structure to path_pipe.sh
øMerge branch 'master' of github.com:adarmitage/pathogen into adarmitage-master

Conflicts:
	path_pipe.sh
	rxlr/parallel_signalp.sh
	rxlr/print_atg_50FaN2.pl
Merge branch 'adarmitage-master'