Page History

• Use the module bioinformatics/blast2go to load the dependencies for BLAST2GO
• This will create an alias runblast2go which incorporates the java options needed for the program.
• A java maxheapsize of 1024m for JAVA is used by default. This can be overridden by setting the environmental variable BLAST2GO_HEAP_SIZE
• The -tempfolder (where logs and temporary files are put) is set to the current working directory. This can be changed with the environmental variable BLAST2GO_TEMP



# /bin/sh
# ----------------Parameters---------------------- #
#$ -S /bin/sh
#$ -q lTb2g.q
#$ -l b2g,mres=6G,h_data=6G,h_vmem=6G
#$ -cwd -j y -N b2g-test -o b2g-test.log
#
# ----------------Modules------------------------- #
#
module load bioinformatics/blast2go
#
# ----------------Your Commands------------------- #
#
echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME
#
#

# Make local copy of cli.prop (this only needs to be done once):
hydracliprop

# Run example dataset:
runblast2go \
  -properties cli.prop \
  -loadfasta example_data/1000_plant.fasta \
  -loadblast example_data/1000_plant_blastResult.xml \
  -mapping \
  -annotation \
  -saveb2g example.b2g \
  -savereport example.pdf

#
echo = `date` job $JOB_NAME done

Anchor
db db

cli.prop and Local Database Access

The file cli.prop gives the settings for the execution of the program. A template configured with the database access information for running BLAST2GO on the Hydra cluster can be copied to your current directory with the command hydracliprop after you load the BLAST2GO module

Anchor
dbpolicy dbpolicy

Local Database Policy

The local database is large and system constraints limit us from keeping old versions. When the database is updated, the old version will no longer be available.

Anchor
stats stats

Outputting Graphs and Statistics

The command line version of BLAST2GO can produce many types of graphs as well as a summary report. The option -statistics all will produce all available statistics as png images, csv and .b2g files. Start BLAST2GO with -statistics (committing any options) to see a list of available charts. The option --savereport <name> creates a PDF with common summary statistics. Creating a combined graph can only be done with the GUI based BLAST2GO Basic which has a free license. This program can also be used to work with the .b2g files created by the command line version.

15 Jun 201714 Nov 2019 MPK