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config_how_to.md

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The configuration file

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

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.

Specification

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.

Example

[TOOL_PATHS]
clustal = /usr/bin/
[DATA]
rfam_dir = /home/user/rfamdir/

Available settings

Setting name with executable(s) which should be accessible from provided location (in brackets).

TOOL_PATHS

  • 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)

DATA

  • 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)