######################################
#  Install C compiler (required for GMAP)
######################################
Xcode in App Store
Launch, preference, download "Command Line Tools"


######################################
# Install wget (required for GMAP)
######################################
# Download latest wget source
> curl -O http://ftp.gnu.org/gnu/wget/wget-1.14.tar.gz

# Uncompress file
> tar -xzf wget-1.14.tar.gz
> ./configure

# Change to the directory
> cd wget-1.14

# Configure 
> ./configure --with-ssl=openssl

# Build the source
> make

# Install wget; ends up in /usr/local/bin/
> sudo make install

# Confirm everything works
> wget --help

# Clean up by removing wget source files
> cd .. && rm -rf wget*

######################################
# Install GMAP 
######################################
# Download
	> curl -O http://research-pub.gene.com/gmap/src/gmap-gsnap-2013-03-05.tar.gz
# Unzip file
	> tar zxvpf gmap-gsnap-2013-03-05.tar.gz
# Change to the directory
	> cd gmap-2013-03-05/
# Configure 
	> ./configure --prefix=/teraraid23/sarah/ --with-gmapdb=/teraraid23/sarah
# Build the source
	> make
# Confirm everything worked
	> make check
# Install
	> make install


######################################
## Make local BLAST server
######################################
> ftp ftp.ncbi.nlm.nih.gov
> anonymous
> email address
> cd blast/executables/blast+/LATEST/
> bin
> get ncbi-blast-2.2.28+-universal-macosx.tar.gz
> bye
> cd desktop
> tar zxvpf ncbi-blast-2.2.27+-universal-macosx.tar.gz

> mc ncbi-blast-2.2.27+ ~/
> nano ~/.profile
	export PATH=/Users/SarahB/ncbi-blast-2.2.27+/bin:${PATH}
ctrl o
return
ctrl x
new terminal session
> which blastn
> nano ~/ .ncbirc
	[NCBI]
	Data=/teraraid23/sarah/.ncbirc
ctrl o
return
ctrl x

######################################
## Make nt database to blast against
######################################
# View pre-formatted databases available on ncbi
> update_blastdb.pl --showall

# Download pre-formatted NR volumes
> /teraraid23/sarah/ncbi-blast-2.2.27+/bin/update_blastdb.pl nr


######################################
## Make blastdb from own fasta files
######################################
# Location of blast nr databases
>cd /var/www/html/blast/db/

# Location of blast 
/home/usr/bin

makeblastdb -in /teraraid23/sarah/Schistosoma/Schistosoma_nt.fasta -input_type fasta -dbtype nucl -out Schistsoma_nt_blastdb