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README
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README
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# webMGA
1. Installation
===============
Besides the scripts within this git repository, several additional packages need to installed
or configured.
1.1 Install and configure NGS project annotation package
The NGS-project is a set of public bioinformatics software tools, reference databases, scripts developed
by our group at UCSD/JCVI for data analysis from metagenomics, RNA-seq, 16S projects.
All the files are included in folder, e.g. /home/some_path/NGS-ann-project, the directory structure
look like:
./NGS-ann-project/NGS-tools/some_scripts
|
-/bin/some_binary_files
|
-/apps/blast+
| /cd-hit
| /other_apps
|
-/refs/db
| /db/Cog*
| /db/Kog*
| /db/Prk*
| /db/Pfam*
| /db/Tigrfam*
| /other_ref_dbs
#### download pre-formatted COG/KOG/PRK databases from NCBI
cd ./NGS-ann-project/refs/db
wget ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/Cog_LE.tar.gz
wget ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/Kog_LE.tar.gz
wget ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/Prk_LE.tar.gz
wget ftp://ftp.ncbi.nlm.nih.gov/pub/COG/COG/fun.txt; mv fun.txt Cog-class
wget ftp://ftp.ncbi.nlm.nih.gov/pub/COG/COG/whog; mv whog Cog-class-info
wget ftp://ftp.ncbi.nlm.nih.gov/pub/COG/KOG/fun.txt; mv fun.txt Kog-class
wget ftp://ftp.ncbi.nlm.nih.gov/pub/COG/KOG/kog; mv kog Kog-class-info
#### unpack these databases
tar xvf Cog_LE.tar.gz
tar xvf Kog_LE.tar.gz
tar xvf Prk_LE.tar.gz
#### dump out the FASTA files, this need blastdbcmd, a program from blast+ package
blastdbcmd -db Cog -outfmt %f -entry all > Cog.faa
blastdbcmd -db Kog -outfmt %f -entry all > Kog.faa
blastdbcmd -db Prk -outfmt %f -entry all > Prk.faa
#### download some additional files
wget ftp://ftp.ncbi.nih.gov/pub/COG/COG2014/data/cognames2003-2014.tab
wget ftp://ftp.ncbi.nih.gov/pub/COG/COG2014/data/fun2003-2014.tab
wget ftp://ftp.ncbi.nih.gov/pub/COG/KOG/fun.txt
#### download Pfam
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
gunzip Pfam-A.hmm.gz
#### hmmpress is a program from hmmer3
hmmpress hmmpress Pfam-A.hmm