tracer.conf

#Configuration file for TraCeR#

[tool_locations]
#paths to tools used by TraCeR for alignment, quantitation, etc
bowtie2_path = /path/to/bowtie2
igblast_path = /path/to/igblastn
kallisto_path = /path/to/kallisto
trinity_path = /path/to/trinity
dot_path = /path/to/dot
neato_path = /path/to/neato

[bowtie2_options]
synthetic_genome_index_path = resources/synthetic_genomes/mouse

[trinity_options]
#line below specifies maximum memory for Trinity Jellyfish component. Set it appropriately for your environment.
max_jellyfish_memory = 1G
#uncomment the line below to explicitly specify Trinity version. Options are '1' or '2'
#trinity_version = 2
#uncomment the line below if you've got a configuration file for Trinity to use a computing grid 
#trinity_grid_conf = /path/to/trinity/grid.conf

#uncomment the line below to explicitly specify Trinity version. Options are '1' or '2'
#trinity_version = 2


[IgBlast_options]
igblast_index_location = resources/igblast_dbs/mouse
imgt_seq_location = resources/imgt_sequences/mouse
igblast_seqtype = TCR

[kallisto_options]
base_transcriptome = /path/to/kallisto/transcriptome