Fix typo in (commented out) test
Sample files for a (commented out) MIRA4 de novo test
Rename a test output file for consistency
Include mirabait wrapper in README file
Use return code for MIRA error conditions

(Need to ignore any stderr output from samtools etc)
Refactor to try to record MIRA to BAM in log file...
This does manage to record the MIRA to BAM output to the log file
Logging tweak
Logging tweak
Avoid writing too much miraconvert output to the log
Report time for MIRA to BAM etc
Tiger mitochondria for mapping tests
Outline clc_mapper test
Fix typo
Remove a TODO comment, already done
Test script to prepare an Arabidopsis thaliana tRNA diagram

$ python fetch_data.py

That should download 10 files (FASTA and an annotation file for each chr),
and merge them to make a 120MB FASTA file and a 31MB tabular file.

$ python chromosome_diagram.py A_thaliana.fasta 5000 A_thaliana_tRNA.tsv 2
3 4 5 1 7 8 "Arabidopsis thaliana" 0 A_thaliana_tRNA.pdf

This should produce a single page PDF file showing the five chromosomes,
with the tRNA shown in red, green, blue (with no background/fill), and
in black with a yellow fill. There should be a single run of NNNN
marked in the middle of chrI.
Correct automated dependency definition for using Biopython
Not pushed to Tool Shed yet, but fix this dependeny too
repository_dependencies.xml --> tool_dependencies.xml for samtools in CLCbio
repository_dependencies.xml --> tool_dependencies.xml for samtools in MIRA4