The configuration file contains pipeline wide settings such are paths to tools and databases used.
It should be used if non-default installation path is used.
Configuration is done using the file config.txt
placed in
INSTALL_LOCATION/rna_blast_analyze/BR_CORE/config.txt
or in custom location
and running the pipeline with the --config_file PATH_to_custom_LOCATION
argument.
There are 3 sections
-
TOOL_PATHS
defines path to executable parent directory
-
DATA
defines paths to data and databases
Each section is specified by its name in square brackets.
[TOOL_PATHS]
clustal = /usr/bin/
[DATA]
rfam_dir = /home/user/rfamdir/
Setting name with executable(s) which should be accessible from provided location (in brackets).
- refold (
refold.pl
) - infernal (
cmalign
,cmbuild
,cmfetch
,cmscan
) - muscle (
muscle
) - clustal (
clustalo
) - locarna (
locarna
) - viennarna_bin (
RNAfold
,RNAalifold
,RNAplot
) - mfold (
hybrid-ss-min
) - centroid (
centroid_homfold
) - turbofold (
TurboFold
)
- rsearch_ribosum
specify full path to RSEARCH matrix file (default: RIBOSUM65.mat
).
- rfam_dir
custom path where Rfam database should be stored. (default: INSTALL_LOCATION/rna_blast_analyze/3rd_party_source/rfamdb/
)
- rfam_url
custom url from where the rfam.cm.gz
(database dump) should be downloaded.
This url is also checked when update is requested (wget timestamp is checked).
(default: ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/rfam.cm.gz
)
- html_template_dir
custom location for html jinja2 template (default: INSTALL_LOCATION/rna_blast_analyze/BR_core/output/
)
- rnastructure_datapath
datapath for RNAstructure (see installation notes for RNAstructure https://rna.urmc.rochester.edu/Text/Thermodynamics.html)