BLASTing your assembled data

First, install a few prerequisites:

sudo apt-get -y install lighttpd blast2 git-core zlib1g-dev

Next, grab things needed for the BLAST server:

sudo pip install pygr whoosh Pillow Jinja2 \
    git+https://github.com/ctb/pygr-draw.git screed
sudo ln -s /usr/bin/blastall /usr/local/bin/

Install the BLAST server and configure it:

cd
git clone https://github.com/ctb/blastkit.git -b 2015-may-nonmodel
sudo ./blastkit/configure-lighttpd.sh

cd blastkit/www
sudo ln -fs $PWD /var/www/blastkit

mkdir files
chmod a+rxwt files
chmod +x /home/ubuntu

cd /home/ubuntu/blastkit
python ./check.py

Now, copy in your newly created transcriptome:

cd /mnt/work
gunzip -c trinity-nematostella-raw.renamed.fasta.gz > /home/ubuntu/blastkit/db/db.fa

cd /home/ubuntu/blastkit
formatdb -i db/db.fa -o T -p F
python index-db.py db/db.fa

You can now access your BLAST server at http://<amazon machine name>/blastkit/.

Note that you will need to enable HTTP access on your Amazon firewall settings; see ../amazon/enable-http.

If you want to use something that will get you results with the test data set, try BLASTing zebrafish lethal giant larvae homolog.

---

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.

---