tracer.conf

#Configuration file for TraCeR#

[tool_locations]
#paths to tools used by TraCeR for alignment, quantitation, etc
#bowtie2_path = /path/to/bowtie2
#bowtie2-build_path = /path/to/bowtie2-build
#igblastn_path = /path/to/igblastn
#makeblastdb_path = /path/to/makeblastdb
#kallisto_path = /path/to/kallisto
#salmon_path = /path/to/salmon
#trinity_path = /path/to/trinity
#dot_path = /path/to/dot
#neato_path = /path/to/neato


[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 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_seqtype = TCR

[base_transcriptomes]
# reference transcriptomes for kallisto/salmon
Mmus = /path/to/kallisto/transcriptome_for_Mmus
Hsap = /path/to/kallisto/transcriptome_for_Hsap

[salmon_options]
# line below specifies type of sequencing library for Salmon; if not specified, automatic detection (--libType A) is used 
#libType = A

# line below specifies minimum acceptable length for valid match in salmon's quasi mapping; if not specified, default value of 31 is used
#kmerLen = 31