We use a config file to pass variables to the IMP engine.
The default parameters are visible in
You could override some parameters via the user configuration file
userconfig.imp.json that you can give
on the runtime.
impy -c /path/to/config.json <command>
Note that if you are entered the docker container with
impy -c /path/to/config.json --enter <command> , this parameter is already set.
Configuration file must be a valid JSON file:
- threads: Number of max threads to use.
- memory_total_gb: Some tools need to set the max memory they could use.
- memory_per_core_gb: Some tools need to set the max memory they could use per cores.
- tmp_dir: Path to a temporary directory.
- raws - Metagenomics: Path to the metagenomics paired files.
- raws - Metatranscriptomics: Path to the metatranscriptomics paired files.
- outputdir: Path to the output directory.
- db_path: Path to the databases.
- preprocessing_filtering: If you want to filter reads from a database. Can be true or false.
- assembler: The assembler to use. Could be idba or megahit.
- pkg_url: Where to download the trimmomatic package to fetch the adapters databases.
- adapter: What adapter to use.
Following parameters are taken from the Trimmomatic documentation:
- leading: Cut bases off the start of a read, if below a threshold quality.
- minlen: Specifies the minimum length of reads to be kept.
- palindrome_clip_threshold: Specifies how accurate the match between the two ‘adapter ligated’ reads must be for PE palindrome read alignment.
- simple_clip_threshold: Specifies how accurate the match between any adapter etc. sequence must be against a read.
- trailing: Specifies the minimum quality required to keep a base.
- seed_mismatch: specifies the maximum mismatch count which will still allow a full match to be performed.
- window_size: Specifies the number of bases to average across.
- window_quality: Specifies the average quality required.
- strictness: This value, which should be set between 0 and 1, specifies the
balance between preserving as much read length as possible vs. removal of incorrect
bases. A low value of this parameter favours longer reads, while a high value favours read correctness.
- target_length: This specifies the read length which is likely to allow the location of the read within the target sequence to be determined.
- jarfile: Path to the trimmomatic JAR file on your system. (You don’t need to set it if you are using the docker container.)
- mink: Minimum k value.
- maxk: Maximum k value.
- step: Increment of k-mer of each iteration.
- perid: Similarity for alignment.
- dimension: 50,
- kmer: 5,
- size: 4,
- theta: 0.5,
- perp: 30,
- cutoff: 1000
- jarfile: Path to the Vizbin JAR file on your system. (You don’t need to set it if you are using the docker container.)
- filter: Name of the filter.
- url: URL to download database.
- pkg_url: Url to download sormerna databases from
- files: Databases to use and index.
- pkg_url: Url to download prokka databases from
- databases: List of databases to use.
- db_ec2pthy and db_hierarchy: Url to download Kegg information from.