bioconda-recipes: Missing busco config file
The current busco recipe correctly installs the dependencies, but leaves out the required config.ini file. It is not terribly difficult to make, but would totally streamline the process to have one included. The default config file is available here: https://gitlab.com/ezlab/busco/blob/master/config/config.ini.default
All of the required paths can be set to the miniconda bin directory:
# BUSCO specific configuration
# It overrides default values in code and dataset cfg, and is overridden by arguments in command line
# Uncomment lines when appropriate
[busco]
# Input file
;in = ./sample_data/target.fa
;# Run name, used in output files and folder
;;out = SAMPLE
;# Where to store the output directory
;;out_path = ./sample_data
;# Path to the BUSCO dataset
;;lineage_path = ./sample_data/example
;# Which mode to run (genome / protein / transcriptome)
;;mode = genome
;# How many threads to use for multithreaded steps
;;cpu = 1
;# Domain for augustus retraining, eukaryota or prokaryota
;# Do not change this unless you know exactly why !!!
;;domain = eukaryota
;# Force rewrite if files already exist (True/False)
;;force = False
;# Restart mode (True/False)
;;restart = False
;# Blast e-value
;;evalue = 1e-3
;# Species to use with augustus, for old datasets only
;;species = fly
;# Augustus extra parameters
;# Use single quotes, like this: '--param1=1 --param2=2'
;;augustus_parameters = ''
;# Tmp folder
;;tmp_path = ./tmp/
;# How many candidate regions (contigs, scaffolds) to consider for each BUSCO
;;limit = 3
;# Augustus long mode for retraining (True/False)
;;long = False
;# Quiet mode (True/False)
;;quiet = False
;# Debug logs (True/False), it needs Quiet to be False
;;debug = True
;# tar gzip output files (True/False)
;;gzip = False
;# Force single core for the tblastn step
;;blast_single_core = True
[tblastn]
# path to tblastn
path = /work-zfs/mschatz1/mschatz/build/miniconda/bin/
[makeblastdb]
# path to makeblastdb
path = /work-zfs/mschatz1/mschatz/build/miniconda/bin/
[augustus]
# path to augustus
path = /work-zfs/mschatz1/mschatz/build/miniconda/bin/
[etraining]
# path to augustus etraining
path = /work-zfs/mschatz1/mschatz/build/miniconda/bin/
;
;# path to augustus perl scripts, redeclare it for each new script
[gff2gbSmallDNA.pl]
path = /work-zfs/mschatz1/mschatz/build/miniconda/bin/
[new_species.pl]
path = /work-zfs/mschatz1/mschatz/build/miniconda/bin/
[optimize_augustus.pl]
path = /work-zfs/mschatz1/mschatz/build/miniconda/bin/
[hmmsearch]
# path to HMMsearch executable
path = /work-zfs/mschatz1/mschatz/build/miniconda/bin/
[Rscript]
# path to Rscript, if you wish to use the plot tool
path = /work-zfs/mschatz1/mschatz/build/miniconda/bin/
Thanks for your help!
Mike
About this issue
- Original URL
- State: closed
- Created 7 years ago
- Comments: 20 (9 by maintainers)
Hello everybody, Im trying to start Busco but im always not able to succes it because im receiving an error message INFO ****************** Start a BUSCO 3.0.2 analysis, current time: 03/12/2018 14:30:57 ****************** INFO Configuration loaded from /gpfs/scratch/cb/khaoula/Tools/busco/scripts/…/config/config.ini INFO Init tools… INFO Check dependencies… ERROR “tblastn” is not accessible, please add or modify its path in the config file. Do not include the commmand in the path ! ERROR BUSCO analysis failed ! ERROR Check the logs, read the user guide, if you still need technical support, then please contact mailto:support@orthodb.org ive tried with Nano to reconfigure the path but it still not working Thank you