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Update IRMA to 1.1.2 #782

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2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -158,7 +158,7 @@ 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/ |
Expand Down
64 changes: 64 additions & 0 deletions irma/1.1.2/Dockerfile
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@@ -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="jarnn@utah.gov"

# 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
29 changes: 29 additions & 0 deletions irma/1.1.2/README.md
Original file line number Diff line number Diff line change
@@ -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)
62 changes: 62 additions & 0 deletions irma/1.1.3/Dockerfile
Original file line number Diff line number Diff line change
@@ -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="jarnn@utah.gov"

# 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
29 changes: 29 additions & 0 deletions irma/1.1.3/README.md
Original file line number Diff line number Diff line change
@@ -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)