Running IRMA
Running IRMA requires proper installation. All assembly options are generally specified by configuration files. Calling IRMA requires three components: (1) a module argument specifying the organism and an optional run-specific configuration, (2) the input fastq data, and (3) the output name for the sample. If more than one fastq are needed per sample, then one needs to concatenate the appropriate read files. GNU zipped (*.fastq.gz) fastq are also valid input. The results will be put in the calling working directory inside a folder with the sample name.
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Paired-end files:
| USAGE: | IRMA <MODULE-config> <R1.fastq.gz/R1.fastq> <R2.fastq.gz/R2.fastq> [path/to]<sample_name> [options] |
| Example 1: | IRMA FLU Sample1_R1.fastq.gz Sample1_R2.fastq.gz Sample1 |
| Example 2: | IRMA EBOLA Patient1_R1.fastq Patient1_R2.fastq /absolute/path/MyPatient |
| Example 3: | IRMA FLU-utr Sample1_R1.fastq.gz Sample1_R2.fastq.gz relative/path/Sample1WithUTRs |
Single read files:
| USAGE: | IRMA <MODULE-config> <fastq/fastq.gz> [path/to/]<sample_name> [options] |
| Example 1: | IRMA FLU SingleEndIllumina.fastq.gz MyIlluminaSample |
| Example 2: | IRMA FLU-pacbio ccs_reads.fastq MyPacBioSample |
| Example 3: | IRMA FLU-pgm pgm_reads.fastq MyIonTorrentSample |
CLI options:
|
--external-config <CONFIG/PATH.sh> -c <CONFIG/PATH.sh> |
Loads an external configuration file to override any other setting. If an invalid setting is supplied IRMA will throw an error. |
The availability of modules (such as FLU and EBOLA) as well as standard configurations (such as FLU-utr) are determined by what has been created by the end-user or developer. To discover what is available, one must traverse the IRMA_RES/modules/ folder. Alternatively, one can view the standard installation structure modules.
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