Merge pull request #899 from Kincekara/irma

update IRMA

README.md

@@ -173,7 +173,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [htslib](https://hub.docker.com/r/staphb/htslib) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/htslib)](https://hub.docker.com/r/staphb/htslib) | <ul><li>[1.14](./htslib/1.14)</li><li>[1.15](./htslib/1.15)</li><li>[1.16](./htslib/1.16)</li><li>[1.17](./htslib/1.17)</li><li>[1.18](./htslib/1.18/)</li><li>[1.19](./htslib/1.19/)</li></ul> | https://www.htslib.org/ |
 | [iqtree](https://hub.docker.com/r/staphb/iqtree/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree)](https://hub.docker.com/r/staphb/iqtree) | <ul><li>1.6.7</li></ul> | http://www.iqtree.org/ |
 | [iqtree2](https://hub.docker.com/r/staphb/iqtree2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/iqtree2)](https://hub.docker.com/r/staphb/iqtree2) | <ul><li>2.1.2</li><li>2.2.2.2</li><li>[2.2.2.6](iqtree2/2.2.2.6/)</li><li>[2.2.2.7](iqtree2/2.2.2.7/)</li></ul> | http://www.iqtree.org/ |
-| [IRMA](https://hub.docker.com/r/staphb/irma/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/irma)](https://hub.docker.com/r/staphb/irma) | <ul><li>1.0.2</li><li>1.0.3</li><li>1.1.2</li><li>1.1.3</li></ul> | https://wonder.cdc.gov/amd/flu/irma/|
+| [IRMA](https://hub.docker.com/r/staphb/irma/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/irma)](https://hub.docker.com/r/staphb/irma) | <ul><li>1.0.2</li><li>1.0.3</li><li>1.1.2</li><li>1.1.3</li><li>[1.1.4](./irma/1.1.4/)</li></ul> | https://wonder.cdc.gov/amd/flu/irma/|
 | [isPcr](https://users.soe.ucsc.edu/~kent/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ispcr)](https://hub.docker.com/r/staphb/ispcr) | <ul><li>[33](ispcr/33/)</li></ul> | https://users.soe.ucsc.edu/~kent/ |
 | [iVar](https://hub.docker.com/r/staphb/ivar/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ivar)](https://hub.docker.com/r/staphb/ivar) | <ul><li>1.1</li><li>1.1 (+SARS-CoV2 reference)</li><li>1.2.1</li><li>1.2.1 (+SC2 ref)</li><li>1.2.2 (+SC2 ref and artic bedfiles)</li><li>1.3</li><li>1.3.1</li><li>1.3.2</li><li>1.4.1</li><li>1.4.2</li></ul> | https://github.com/andersen-lab/ivar |
 | [Kaptive](https://hub.docker.com/r/staphb/kaptive/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kaptive)](https://hub.docker.com/r/staphb/kaptive) | <ul><li>[2.0.0](./kaptive/2.0.0/)</li><li>[2.0.3](./kaptive/2.0.3/)</li><li>[2.0.5](./kaptive/2.0.5/)</li><li>[2.0.8](./kaptive/2.0.8/)</li></ul> | https://github.com/klebgenomics/Kaptive |

irma/1.1.4/Dockerfile

@@ -0,0 +1,45 @@
+FROM ubuntu:jammy as app
+
+ARG IRMA_VER="1.1.4"
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="IRMA"
+LABEL software.version=$IRMA_VER
+LABEL description="IRMA was designed for the robust assembly, variant calling, and phasing of highly variable RNA viruses. Currently IRMA is deployed with modules for influenza, ebolavirus and coronavirus."
+LABEL website="https://wonder.cdc.gov/amd/flu/irma/"
+LABEL license="https://wonder.cdc.gov/amd/flu/irma/disclaimer.html"
+LABEL maintainer="John Arnn"
+LABEL maintainer.email="[email protected]"
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    perl \
+    r-base \
+    unzip \
+    wget && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# install IRMA
+RUN wget https://wonder.cdc.gov/amd/flu/irma/flu-amd-202402.zip &&\
+    unzip flu-amd-202402.zip &&\
+    rm flu-amd-202402.zip
+
+ENV PATH="${PATH}:/flu-amd" \
+    LC_ALL=C
+
+CMD ["IRMA"]
+
+WORKDIR /data
+
+## Test ##
+FROM app as test
+
+RUN cd /flu-amd/tests && \
+    ./test_run.sh
+
+RUN wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR179/072/SRR17940172/SRR17940172_1.fastq.gz && \
+    wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR179/072/SRR17940172/SRR17940172_2.fastq.gz 
+
+RUN IRMA FLU SRR17940172_1.fastq.gz SRR17940172_2.fastq.gz SRR17940172

irma/1.1.4/README.md

@@ -0,0 +1,37 @@
+# IRMA container
+Main tool: [IRMA](https://wonder.cdc.gov/amd/flu/irma/)
+
+Basic information on how to use this tool:
+- executable: IRMA
+- help: 
+- version:
+- description: IRMA was designed for the robust assembly, variant calling, and phasing of highly variable RNA viruses. Currently IRMA is deployed with modules for influenza, ebolavirus and coronavirus. 
+
+Additional information:
+
+The IRMA team at the CDC maintain a docker image as well at https://hub.docker.com/r/cdcgov/irma. The StaPH-B docker image is not maintained by IRMA developers at the CDC, so if users encounter issues with this docker image specifically they should file an issue on this github repo and do not contact CDC for support.
+
+Full documentation: https://wonder.cdc.gov/amd/flu/irma/
+
+# Example Usage
+```{bash}
+# Paired-end files:
+# USAGE:	IRMA <MODULE-config> <R1.fastq.gz/R1.fastq> <R2.fastq.gz/R2.fastq> <sample_name>
+
+IRMA FLU Sample1_R1.fastq.gz Sample1_R2.fastq.gz Sample1
+
+IRMA EBOLA Patient1_R1.fastq Patient1_R2.fastq MyPatient
+
+IRMA FLU-utr Sample1_R1.fastq.gz Sample1_R2.fastq.gz Sample1WithUTRs
+
+# Single read files:
+# USAGE:	IRMA <MODULE-config> <fastq/fastq.gz> <sample_name>
+
+IRMA FLU SingleEndIllumina.fastq.gz MyIlluminaSample
+
+IRMA FLU-pacbio ccs_reads.fastq MyPacBioSample
+
+IRMA FLU-pgm pgm_reads.fastq MyIonTorrentSample
+
+```
+