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README_BAGEL4_SETUP_and_RUN.txt
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README_BAGEL4_SETUP_and_RUN.txt
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BAGEL4 v.1.0 July 2018
---------- SOFTWARE dependencies ----------
perl
hmmsearch3
blastall
glimmer3
librsvg2-bin
PfamScan # this program is included in the BAGEL4.tar or download the latest version from ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Tools/
---------- DATABASE dependencies ----------
PFAM-A database:
- HOW TO INSTALL PFAM database
- get the latest release from: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/ ....../Pfam-A.hmm.gz
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam31.0/Pfam-A.hmm.gz
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam31.0/Pfam-A.fasta.gz
wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam31.0/Pfam-A.seed
- Unzip the files
gunzip Pfam*.gz
- create index binaries
hmmpress Pfam-A.hmm
- Index Pfam-A.fasta for BLAST searches
formatdb -i Pfam-A.fasta -p T
optional download: uniref_db = uniref50.fasta
---------- INSTALLING BAGEL ----------
unpack BAGEL4.tar in e.g. /usr/bagel4
---------- CONFIGURATION ----------
Open the bagel4.conf
- change the PFAM database location if needed
- change the default number of cpu's (threads)
- for optimal performance of BAGEL keep the other setting untouched
LIBRARIES
- if BAGEL is installed in an other folder then /usr/bagel4 do the following:
- open bagel4.pl to set proper path for the BAGEL4 program
- edit line: use lib "/usr/bagel4/lib";
- edit line: my %conf = read_conf('/usr/bagel4/bagel4.conf') ;
---------- TOOLS ------------------
Make symbolic link in MOODS folder
cd tools/MOODS-python-1.9.3/scripts
ln -s ../MOODS/
---------- UPDATING BAGEL ----------
---------- EXECUTING BAGEL ----------
There are two program to run BAGEL:
1. bagel4.pl is the main program and can handle single files
bagel4.pl
-s Sessiondir [default=current folder]
-i input file should be a DNA file in the FASTA format
-r NCBI reference genome
-is_circular [default=1 for yes]
-glimmer [default=0, 1 means that the training model is present in the sessiondir; normally made by bagel3_wrapper.pl]
-graphics [default=1, 1 means that a graphic is drawn of the AOI]
-o output file [default=results.txt]
2. bagel4_wrapper.pl is a wrapper around bagel4.pl and screens packed files (zip, rar) or folders recursively based on a regular expression
bagel4_wrapper.pl
-s Sessiondir [default=./my_session]
-i queryfolder or zip_file containing DNA files in the FASTA format
-webserver [default=0; Meaning that the analysis will de done on the folder given after -i, else a query from the webserver is expected]
-glimmer make glimmer model [default=1; means that a global model will be made] Usefull for multiple entry FastA files with relative small DNA fragments
-r regular expression for identifing files [default=.* meaning all files ]
NOTE: executing bagel4.pl or bagel4_wrapper.pl without parameters will give you the list of options needed to run these programs
---------- EXAMPLES ----------
most basic option to execute BAGEL
e.g. ./bagel4.pl -i /var/genomes/Lactococcus_lactis_cremoris_MG1363_uid58837/NC_009004.fna
e.g. ./bagel4_wrapper.pl -i /var/genomes/Lactococcus_lactis_cremoris_MG1363_uid58837 -r \.fna\$
e.g. ./bagel4_wrapper.pl -i /var/dna/myfolder -r \.fna\$
================================
Anne de Jong and Auke van Heel
university of Groningen
Nijenborgh 7
9743 AG Groningen
the Netherlands
July 2018
================================