Now using the BAM datatype for testing with TravisCI
Didn't close XML tag, might as well include BAM to BAI converter too?
Remove commented MIRA3 test example from MIRA4 wrapper (will need alternative)
Specific error message if Galaxy hasn't indexed the BAM file

This can happen due to a Galaxy bug or configuration problem which
assumes samtools is on the PATH (observed on the Test Tool Shed).
Minor markup polish in README file
Markup polish; MIRA4 test instructions
Example 26 reads in FASTQ format from MIRA4's minidemo/demo4
MIRA 4.0 RC4 de novo assembly of U13small_m.fastq (unpaired Sanger)
Commented out test for mira4_de_novo.xml (framework can't cope yet)
Use SQLite template to speedup tests on TravisCI (avoids migration steps)
Declare dependency on samtools
Should be using tool_dependencies.xml here
Mark this script as executable
Sample paired Illumina HiSeq 2000 reads from SRR639755

$ wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/SRR639755/SRR639755_1.fastq.gz
$ wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR639/SRR639755/SRR639755_2.fastq.gz
$ ~/picobio/blooming_reads/interlace_fastq.py SRR639755_1.fastq.gz SRR639755_2.fastq.gz | gzip > SRR639755_12.fastq.gz
Interlacing SRR639755_1.fastq.gz and SRR639755_2.fastq.gz
Decompressing SRR639755_1.fastq.gz
Decompressing SRR639755_2.fastq.gz
Interlacing paired FASTQ files to stdout...
Interlacing paired FASTQ files done.

That gives us an interlaced FASTQ file with /1 and /2 naming. Select mitochondria reads:

$ mirabait -f fastq -t fastq NC_010642.fasta SRR639755_12.fastq.gz SRR639755_12_mito
...

The FASTQ file is still sorted, but now a mix of pairs and orphans which some tools hate:

$ ~/pico_galaxy/tools/fastq_paired_unpaired/fastq_paired_unpaired.py sanger SRR639755_12_mito.fastq SRR639755_mito_pairs.fastq SRR639755_mito_orphans.fastq
1965 reads (965 forward, 1000 reverse), 1064 in pairs, 901 as singles
Commented out tests for mira4_de_novo.xml
Simple test for mira4_de_novo.xml (failing)

$ ./run_functional_tests.sh -id mira_4_0_de_novo
...
======================================================================
ERROR: MIRA v4.0 de novo assember ( mira_4_0_de_novo ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
  File /mnt/galaxy/galaxy-central/test/functional/test_toolbox.py, line 216, in test_tool
    self.do_it( td, shed_tool_id=shed_tool_id )
  File /mnt/galaxy/galaxy-central/test/functional/test_toolbox.py, line 25, in do_it
    data_list = self.__run_tool( testdef )
  File /mnt/galaxy/galaxy-central/test/functional/test_toolbox.py, line 106, in __run_tool
    page_inputs = self.__expand_grouping(testdef.tool.inputs_by_page[0], all_inputs)
  File /mnt/galaxy/galaxy-central/test/functional/test_toolbox.py, line 172, in __expand_grouping
    expanded_inputs.update( self.__expand_grouping( { new_prefix : r_value }, declared_inputs, prefix=new_prefix ) )
  File /mnt/galaxy/galaxy-central/test/functional/test_toolbox.py, line 159, in __expand_grouping
    if declared_inputs[ value.test_param.name ] == case.value:
KeyError: 'type'
...
Clarify manual install instructions
Sample test output for CLCbio assembler
Outline test for clc_assembler.xml (needs test framework fixes)
Update travis configuration to target my API driven testing branch.