Install BLAST+ v2.2.27 under TravisCI
Change Tool Shed dependencies to BLAST+ v2.2.27
Regenerate blastn_rhodopsin_vs_three_human.tabular using BLAST+ 2.2.27

$ blastn -query rhodopsin_nucs.fasta -subject three_human_mRNA.fasta -task megablast -evalue 1e-40 -out blastn_rhodopsin_vs_three_human.tabular -outfmt 6
Regenerate blastp_four_human_vs_rhodopsin.xml with BLAST+ 2.2.27

$ blastp -query four_human_proteins.fasta -subject rhodopsin_proteins.fasta -task blastp -evalue 1e-08 -out blastp_four_human_vs_rhodopsin.xml -outfmt 5 -seg no -matrix BLOSUM62 -parse_deflines
Regenerate blastx_rhodopsin_vs_four_human.xml with BLAST+ 2.2.27

$ blastx -query rhodopsin_nucs.fasta -subject four_human_proteins.fasta -query_gencode 1 -evalue 1e-10 -out blastx_rhodopsin_vs_four_human.xml -outfmt 5
Regenerate blastx_rhodopsin_vs_four_human.tabular with BLAST+ 2.2.27

$ blastx -query rhodopsin_nucs.fasta -subject four_human_proteins.fasta -query_gencode 1 -evalue 1e-10 -out blastx_rhodopsin_vs_four_human.tabular -outfmt 6
Regenerate blastx_rhodopsin_vs_four_human_ext.tabular with BLAST+ 2.2.27

$ blastx -query rhodopsin_nucs.fasta -subject four_human_proteins.fasta -query_gencode 1 -evalue 1e-10 -out blastx_rhodopsin_vs_four_human_ext.tabular -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
Regenerate tblastn_four_human_vs_rhodopsin.xml with BLAST+ 2.2.27

$ tblastn -query four_human_proteins.fasta -subject rhodopsin_nucs.fasta -evalue 1e-10 -out tblastn_four_human_vs_rhodopsin.xml -outfmt 5 -db_gencode 1 -seg no -matrix BLOSUM80
Regenerate tblastn_four_human_vs_rhodopsin.html with BLAST+ 2.2.27

$ tblastn -query four_human_proteins.fasta -subject rhodopsin_nucs.fasta -evalue 1e-10 -out tblastn_four_human_vs_rhodopsin.html -outfmt 0 -html -db_gencode 1 -seg no -matrix BLOSUM80
Update BLAST XML to tabular output with revised BLASTX output from BLAST+ 2.2.27

$ python /mnt/galaxy/galaxy-central/tools/ncbi_blast_plus/blastxml_to_tabular.py blastx_rhodopsin_vs_four_human.xml blastx_rhodopsin_vs_four_human_converted.tabular std

$ python /mnt/galaxy/galaxy-central/tools/ncbi_blast_plus/blastxml_to_tabular.py blastx_rhodopsin_vs_four_human.xml blastx_rhodopsin_vs_four_human_converted_ext.tabular ext