BAGEL4 v.1.2 June 2022
To download all dependencies use http://ngs.molgenrug.nl/bagel4/
---------- SOFTWARE dependencies ----------
perl5,
hmmsearch3,
blastall,
glimmer3,
librsvg2-bin,
PfamScan # 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
---------- CONFIGURATION ----------
Open the bagel4.conf
- Adapt folder locations to your system
- Optionally change the default number of cpu's (threads)
- For optimal performance of BAGEL keep the other setting untouched
---------- LIBRARIES ----------
Add the BAGEL4 library to PERL5LIB: e.g., export PERL5LIB=/data/pg-molgen/software/bagel4/lib
Or copy the files from the bagel4/lib to your perl5 lib folder ( e.g., /usr/lib/perl5)
---------- TOOLS ------------------
Make symbolic link in MOODS folder in the BAGEL4 program dir
cd tools/MOODS-python-1.9.3/scripts
ln -s ../MOODS/
---------- UPDATING BAGEL ----------
https://github.com/annejong/BAGEL4
---------- EXECUTING BAGEL ----------
To run BAGEL:
bagel4_wrapper.pl is a wrapper around all files in a folder or subfolder and also will screens packed files (zip, rar) or folders recursively based on a regular expression
Without parameters bagel4_wrapper.pl the options will be listed:
-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 ]
---------- EXAMPLES ----------
most basic option to execute BAGEL
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$
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Anne de Jong and Auke van Heel
university of Groningen
Nijenborgh 7
9743 AG Groningen
the Netherlands
anne.de.jong@rug.nl
June 2022
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