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BAGEL4

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$


================================

Anne de Jong and Auke van Heel
university of Groningen
Nijenborgh 7
9743 AG Groningen
the Netherlands
[email protected]

June 2022

================================

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