From 1e9f1ea89d700fbdc07b222157c26be3d1cdc522 Mon Sep 17 00:00:00 2001 From: Young Date: Fri, 27 Dec 2024 12:33:43 -0700 Subject: [PATCH 1/2] fixing Dockerfile filepath for GA (#1163) --- .github/workflows/update_freyja.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/update_freyja.yml b/.github/workflows/update_freyja.yml index a0e546937..f0c8a4a68 100644 --- a/.github/workflows/update_freyja.yml +++ b/.github/workflows/update_freyja.yml @@ -28,7 +28,7 @@ jobs: version=1.5.2 echo "version=$version" >> $GITHUB_OUTPUT - file=build-files/freyja/$version/Dockerfile + file=build-files/freyja/1.5.2-bf/Dockerfile ls $file echo "file=$file" >> $GITHUB_OUTPUT From afab061efae136f682e2bb694dc5b83b8485151e Mon Sep 17 00:00:00 2001 From: Young Date: Fri, 27 Dec 2024 12:57:09 -0700 Subject: [PATCH 2/2] Adding fastplong (#1162) * adding fastplong * adding fastplong version 0.2.2 * fixed hardcoded version * Update Dockerfile line 54: wget -q --------- Co-authored-by: Kutluhan Incekara <46578029+Kincekara@users.noreply.github.com> --- Program_Licenses.md | 1 + README.md | 1 + build-files/fastplong/0.2.2/Dockerfile | 57 ++++++++++++++++++++++++++ build-files/fastplong/0.2.2/README.md | 20 +++++++++ 4 files changed, 79 insertions(+) create mode 100644 build-files/fastplong/0.2.2/Dockerfile create mode 100644 build-files/fastplong/0.2.2/README.md diff --git a/Program_Licenses.md b/Program_Licenses.md index 173ea984a..65c038f9b 100644 --- a/Program_Licenses.md +++ b/Program_Licenses.md @@ -55,6 +55,7 @@ The licenses of the open-source software that is contained in these Docker image | FastANI | Apache v2.0 | https://github.com/ParBLiSS/FastANI/blob/master/LICENSE | | fasten | MIT | https://github.com/lskatz/fasten/blob/master/LICENSE | | Fastp | MIT | https://github.com/OpenGene/fastp/blob/master/LICENSE | +| Fastplong | MIT | https://github.com/OpenGene/fastplong/blob/main/LICENSE | | FastTree | GNU GPLv2 | http://www.microbesonline.org/fasttree/ | | FastQC | GNU GPLv3 | https://github.com/s-andrews/FastQC/blob/master/LICENSE.txt | | fastq-scan | MIT | https://github.com/rpetit3/fastq-scan/blob/master/LICENSE | diff --git a/README.md b/README.md index c9a0326d6..260ad6af2 100644 --- a/README.md +++ b/README.md @@ -166,6 +166,7 @@ To learn more about the docker pull rate limits and the open source software pro | [FastANI](https://hub.docker.com/r/staphb/fastani)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fastani)](https://hub.docker.com/r/staphb/fastani) | | https://github.com/ParBLiSS/FastANI | | [fasten](https://hub.docker.com/r/staphb/fasten)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fasten)](https://hub.docker.com/r/staphb/fasten) | | https://github.com/lskatz/fasten | | [Fastp](https://hub.docker.com/r/staphb/fastp)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fastp)](https://hub.docker.com/r/staphb/fastp) | | http://opengene.org/fastp/
https://github.com/OpenGene/fastp | +| [fastplong](https://hub.docker.com/r/staphb/fastplong)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fastplong)](https://hub.docker.com/r/staphb/fastplong) | | https://github.com/OpenGene/fastplong | | [FastTree](https://hub.docker.com/r/staphb/fasttree)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fasttree)](https://hub.docker.com/r/staphb/fasttree) | | http://www.microbesonline.org/fasttree/ | | [FastQC](https://hub.docker.com/r/staphb/fastqc)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fastqc)](https://hub.docker.com/r/staphb/fastqc) | | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
https://github.com/s-andrews/FastQC | | [fastq-scan](https://hub.docker.com/r/staphb/fastq-scan)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fastq-scan)](https://hub.docker.com/r/staphb/fastq-scan) | | https://github.com/rpetit3/fastq-scan | diff --git a/build-files/fastplong/0.2.2/Dockerfile b/build-files/fastplong/0.2.2/Dockerfile new file mode 100644 index 000000000..9c82ba0e5 --- /dev/null +++ b/build-files/fastplong/0.2.2/Dockerfile @@ -0,0 +1,57 @@ +ARG FASTPLONG_VER="0.2.2" + +FROM ubuntu:jammy AS app + +# List all software versions are ARGs near the top of the dockerfile +# 'ARG' sets environment variables during the build stage +# ARG variables are ONLY available during image build, they do not persist in the final image +ARG FASTPLONG_VER + +# 'LABEL' instructions tag the image with metadata that might be important to the user +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="fastplong" +LABEL software.version="${FASTPLONG_VER}" +LABEL description="Ultrafast preprocessing and quality control for long reads" +LABEL website="https://github.com/OpenGene/fastplong" +LABEL license="https://github.com/OpenGene/fastplong/blob/main/LICENSE" +LABEL maintainer="Erin Young" +LABEL maintainer.email="eriny@utah.gov" + +# 'RUN' executes code during the build +# Install dependencies via apt-get or yum if using a centos or fedora base +RUN apt-get update && apt-get install -y --no-install-recommends \ + libdeflate-dev \ + libisal-dev \ + libhwy-dev \ + wget && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN wget --no-check-certificate -q http://opengene.org/fastplong/fastplong.${FASTPLONG_VER} && \ + mv fastplong.${FASTPLONG_VER} /usr/local/bin/fastplong && \ + chmod a+x /usr/local/bin/fastplong + +# 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.' +CMD [ "fastplong", "--help" ] + +# 'WORKDIR' sets working directory +WORKDIR /data + +##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ##### +##### Step 2. Set up the testing stage. ##### +##### The docker image is built to the 'test' stage before merging, but ##### +##### the test stage (or any stage after 'app') will be lost. ##### +##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ##### + +# A second FROM insruction creates a new stage +FROM app AS test + +# set working directory so that all test inputs & outputs are kept in /test +WORKDIR /test + +RUN fastplong --help + +RUN wget --no-check-certificate -q https://zenodo.org/records/10733190/files/df_test_files.tar.gz && \ + tar -xvf df_test_files.tar.gz && \ + fastplong -i test_files/test.fastq.gz -o filtered.test.fastq.gz && \ + ls filtered.test.fastq.gz diff --git a/build-files/fastplong/0.2.2/README.md b/build-files/fastplong/0.2.2/README.md new file mode 100644 index 000000000..2fe0b104a --- /dev/null +++ b/build-files/fastplong/0.2.2/README.md @@ -0,0 +1,20 @@ +# fastplong container + +Main tool: [fastplong](https://github.com/OpenGene/fastplong) + +Code repository: https://github.com/OpenGene/fastplong + +Basic information on how to use this tool: +- executable: fastplong +- help: --help +- version: --version +- description: | +> Ultrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.). + +Full documentation: https://github.com/OpenGene/fastplong + +## Example Usage + +```bash +fastplong -i input.fastq.gz -o output.fastq.gz +```