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\$


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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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