Create rule to download and setup panX data

[mbhall88]

This will be based on the following code.

wget http://pangenome.tuebingen.mpg.de/dataset/Escherichia_coli/all_gene_alignments.tar.gz -O - | tar xzf -
cd all_gene_alignments
# delete all protein alignments
find . -name '*_aa_*' | xargs -I @ rm @
# filter into subfolders
# outnum generates the name of the output directory
outnum=0
# n is the number of files we have moved
n=0

# Go through all fasta files in the current directory
for f in *.fa.gz; do
   # Create new output directory if first of new batch of 4000
   if [ $n -eq 0 ]; then
      outdir="$outnum"
      mkdir "$outdir"
      ((outnum++))
   fi
   # Move the file to the new subdirectory
   mv "$f" "$outdir"

   # Count how many we have moved to there
   ((n++))

   # Start a new output directory if we have sent 4000
   [ $n -eq 4000 ] && n=0
done

[mbhall88]

As the generation of the filenames for the pipeline relies on the gene alignments being present it doesn't make sense to have the data setup as part of the pipeline. Snakemake requires the files to be present before running the pipeline.