Iterative Refinement Meta-Assembler (IRMA) version 0.6.7 built from IRMA v0.6.7 zip file from the IRMA Website.

From the IRMA Website:

IRMA was designed for the robust assembly, variant calling, and phasing of highly variable RNA viruses. Currently IRMA is deployed with modules for influenza and ebolavirus. IRMA is free to use and parallelizes computations for both cluster computing and single computer multi-core setups. Please refer to our FAQ below or contact us for further questions. Please read IRMA's full license and disclaimer.

The IRMA manuscript provides more background on the methodology.

NOTE: the SAM binaries packaged within LABEL and the BLAT binaries packaged within IRMA may be used for government and/or academic use only. Commercial use and redistribution of SAM or BLAT is excluded without permission from their authors. Please read the SAM license and BLAT license.

Install Singularity

Run from Singularity Hub

 singularity run shub://peterk87/irma-singularity

The following steps are needed to use the image:

1. Pull the image

singularity pull --name TMP_DIRECTORY shub://peterk87/irma-singularity@latest

This will command will create a file irma-singularity.simg, which is executable.

2. Use the image

./irma-singularity.simg --help

singularity pull --name TMP_DIRECTORY shub://peterk87/irma-singularity/@VERSION.NUMBER

1. Create a singularity folder:

mkdir HOME/singularity

2. Pull the image to the singularity folder.

singularity pull --name sistr shub://peterk87/irma-singularity@latest

3. Link the image to a folder in your $PATH (e.g. $HOME/bin)

ln -s $HOME/singularity/irma.simg $HOME/bin/IRMA

4. Now, when you login again, you should be able to just type:

IRMA

Output:

Welcome to IRMA 0.6.7
IRMA installed on 2019-02-19
Iterative Refinement Meta-Assembler (IRMA), v0.6.7 (13 APR 2017)
Samuel S. Shepard (NCIRD/OID/CDC), [email protected]

GPL version 3. This program comes with ABSOLUTELY NO WARRANTY. This is free software.
You are welcome to redistribute it under certain conditions. See:  <http://www.gnu.org/licenses/>.
Components of this pipeline have non-commercial restrictions. See: IRMA_RES/scripts/packaged-citations-licenses

USAGE:
(PAIRED-END):   IRMA <MODULE|MODULE-CONFIG> <R1.fastq.gz|R1.fastq> <R2.fastq.gz|R2.fastq> <sample_name>
(SINGLE-END):   IRMA <MODULE|MODULE-CONFIG> <fastq|fastq.gz> <sample_name>