cd /Volumes/Bay3/Software

cd ncbi-blast-2.2.27+/bin/

ls

./blastn

run blastn

!blastn

cd ..

ls

cd bin

ls

!blastn

cd ..


cd ..

cd ncbi-blast-2.2.26+/

ls

cd ..

cd ..
This next command was key!

h/t 

http://nbviewer.ipython.org/urls/raw.github.com/ngs-docs/ngs-notebooks/rendered/ngs-10-blast.ipynb
cp ncbi-blast-2.2.27+/bin/* /usr/local/bin

!blastn

!makeblasdb

!makeblastdb

!makeblastdb -in /Users/sr320/Desktop/QPX_transcriptome_v1.fasta -dbtype nucl -out /Volumes/Bay3/Software/ncbi-blast-2.2.27\+/db/QPX_tran_v1plos

!makeblastdb -in /Users/sr320/Desktop/QPX_v015.fasta -dbtype nucl -out /Volumes/Bay3/Software/ncbi-blast-2.2.27\+/db/QPX_v015

!blastn -query /Users/sr320/Desktop/QPX_transcriptome_v1.fasta -db /Volumes/Bay3/Software/ncbi-blast-2.2.27\+/db/QPX_v015 -out /Volumes/web/cnidarian/QPX_trans_blastn_genome -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -num_threads 2 -task blastn

head /Volumes/web/cnidarian/QPX_trans_blastn_genome

!head /Volumes/web/cnidarian/QPX_trans_blastn_genome