Merge pull request #782 from jwarnn/master

Update IRMA to 1.1.2

README.md

@@ -159,7 +159,7 @@ 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</li><li>1.15</li><li>1.16</li><li>1.17</li><li>[1.18](htslib/1.18/)</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></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></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></ul> | https://wonder.cdc.gov/amd/flu/irma/|
 | [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</li><li>2.0.3</li><li>2.0.5</li></ul> | https://github.com/katholt/Kaptive/ |
 | [Kleborate](https://hub.docker.com/r/staphb/kleborate/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kleborate)](https://hub.docker.com/r/staphb/kleborate) | <ul><li>2.0.4</li><li>2.1.0</li><li>2.2.0</li><li>2.3.2</li><li>[2.3.2-2023-05](kleborate/2.3.2-2023-05/README.md)</li></ul> | https://github.com/katholt/Kleborate/ <br/> https://github.com/katholt/Kaptive/ |

irma/1.1.2/Dockerfile

@@ -0,0 +1,64 @@
+# FROM defines the base docker image. This command has to come first in the file
+# The 'as' keyword lets you name the folowing stage. We use `app` for the production image
+FROM --platform=linux/x86_64 ubuntu:focal as app
+
+# ARG sets environment variables during the build stage
+ARG IRMA_VER="1.1.2"
+
+# LABEL instructions tag the image with metadata that might be important to the user
+# Optional, but highly recommended
+LABEL base.image="ubuntu:xenial"
+LABEL dockerfile.version="3"
+LABEL software="IRMA"
+LABEL software.version=$IRMA_VER
+LABEL description="IRMA was designed for the robust assembly, variant calling, and phasing of highly variable RNA viruses. Currently IRMA is deployed with modules for influenza, ebolavirus and coronavirus."
+LABEL website="https://wonder.cdc.gov/amd/flu/irma/"
+LABEL license="https://wonder.cdc.gov/amd/flu/irma/disclaimer.html"
+LABEL maintainer="John Arnn"
+LABEL maintainer.email="[email protected]"
+
+# RUN executes code during the build
+# Install dependencies via apt-get or yum if using a centos or fedora base
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && apt-get install -y --no-install-recommends \
+ perl \
+ default-jre \
+ apt-transport-https \
+ ca-certificates \
+ gnupg \
+ libcurl4-openssl-dev \
+ libssl-dev \
+ libxml2 \
+ libxml2-dev \
+ libncurses5 \
+ wget \
+ gzip \
+ git && \
+ apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# IRMA Needs R
+RUN  apt-get update && apt-get -y upgrade && apt-get -y install r-base \
+  r-base-dev
+
+ # install IRMA
+RUN wget https://wonder.cdc.gov/amd/flu/irma/flu-amd-202310.zip && \
+  unzip flu-amd-202310.zip && \
+  rm flu-amd-202310.zip && \
+  chmod 755 -R flu-amd && \
+  mkdir data
+
+# set the environment
+ENV PATH="${PATH}:/flu-amd"
+
+# WORKDIR sets working directory
+WORKDIR /data
+
+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 && gzip -d SRR17940172_1.fastq.gz && \
+    wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR179/072/SRR17940172/SRR17940172_2.fastq.gz && gzip -d SRR17940172_2.fastq.gz
+
+RUN IRMA FLU SRR17940172_1.fastq SRR17940172_2.fastq SRR17940172

irma/1.1.2/README.md

@@ -0,0 +1,29 @@
+# IRMA container
+Main tool: [IRMA](https://wonder.cdc.gov/amd/flu/irma/)
+
+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. 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.
+
+# 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
+
+```
+Better documentation can be found at https://wonder.cdc.gov/amd/flu/irma/](https://wonder.cdc.gov/amd/flu/irma/
+
+The manuscript can be found at [https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3030-6](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3030-6)

irma/1.1.3/Dockerfile

@@ -0,0 +1,62 @@
+# FROM defines the base docker image. This command has to come first in the file
+# The 'as' keyword lets you name the folowing stage. We use `app` for the production image
+FROM --platform=linux/x86_64 ubuntu:focal as app
+
+# ARG sets environment variables during the build stage
+ARG IRMA_VER="1.1.3"
+
+# LABEL instructions tag the image with metadata that might be important to the user
+# Optional, but highly recommended
+LABEL base.image="ubuntu:xenial"
+LABEL dockerfile.version="4"
+LABEL software="IRMA"
+LABEL software.version=$IRMA_VER
+LABEL description="IRMA was designed for the robust assembly, variant calling, and phasing of highly variable RNA viruses. Currently IRMA is deployed with modules for influenza, ebolavirus and coronavirus."
+LABEL website="https://wonder.cdc.gov/amd/flu/irma/"
+LABEL license="https://wonder.cdc.gov/amd/flu/irma/disclaimer.html"
+LABEL maintainer="John Arnn"
+LABEL maintainer.email="[email protected]"
+
+# RUN executes code during the build
+# Install dependencies via apt-get or yum if using a centos or fedora base
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && apt-get install -y --no-install-recommends \
+ perl \
+ default-jre \
+ apt-transport-https \
+ ca-certificates \
+ gnupg \
+ libcurl4-openssl-dev \
+ libssl-dev \
+ libxml2 \
+ libxml2-dev \
+ libncurses5 \
+ wget && \
+ apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+# IRMA Needs R
+RUN  apt-get update && apt-get -y upgrade && apt-get -y install r-base \
+  r-base-dev
+
+ # install IRMA
+RUN wget https://wonder.cdc.gov/amd/flu/irma/flu-amd-202311.zip && \
+  unzip flu-amd-202311.zip && \
+  rm flu-amd-202311.zip && \
+  chmod 755 -R flu-amd && \
+  mkdir data
+
+# set the environment
+ENV PATH="${PATH}:/flu-amd"
+
+# WORKDIR sets working directory
+WORKDIR /data
+
+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/1.1.3/README.md

@@ -0,0 +1,29 @@
+# IRMA container
+Main tool: [IRMA](https://wonder.cdc.gov/amd/flu/irma/)
+
+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. 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.
+
+# 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
+
+```
+Better documentation can be found at [https://wonder.cdc.gov/amd/flu/irma/](https://wonder.cdc.gov/amd/flu/irma/)
+
+The manuscript can be found at [https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3030-6](https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3030-6)