diff --git a/Program_Licenses.md b/Program_Licenses.md index 76f72e242..b51a18b87 100644 --- a/Program_Licenses.md +++ b/Program_Licenses.md @@ -90,6 +90,7 @@ The licenses of the open-source software that is contained in these Docker image | NCBI Datasets | Public Domain | https://github.com/ncbi/datasets/blob/master/pkgs/ncbi-datasets-cli/LICENSE.md | | NCBI table2asn | Public Domain | unknown | | ngmaster | GNU GPLv3 | https://github.com/MDU-PHL/ngmaster/blob/master/LICENSE | +| ONTime | MIT | https://github.com/mbhall88/ontime/blob/main/LICENSE | | OrthoFinder | GNU GPLv3 | https://github.com/davidemms/OrthoFinder/blob/master/License.md | | Panaroo | MIT | https://github.com/gtonkinhill/panaroo/blob/master/LICENSE | | Pangolin | GNU GPLv3 | https://github.com/cov-lineages/pangolin/blob/master/LICENSE.txt | diff --git a/README.md b/README.md index cd3f95fb1..0b04a691f 100644 --- a/README.md +++ b/README.md @@ -193,6 +193,7 @@ To learn more about the docker pull rate limits and the open source software pro | [NCBI Datasets](https://hub.docker.com/r/staphb/ncbi-datasets)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-datasets)](https://hub.docker.com/r/staphb/ncbi-datasets) |
Click to see all datasets versions **datasets versions** | [https://github.com/ncbi/datasets](https://github.com/ncbi/datasets)
[https://www.ncbi.nlm.nih.gov/datasets/docs/v1/](https://www.ncbi.nlm.nih.gov/datasets/docs/v1/) | | [NCBI AMRFinderPlus](https://hub.docker.com/r/staphb/ncbi-amrfinderplus)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-amrfinderplus)](https://hub.docker.com/r/staphb/ncbi-amrfinderplus) | **AMRFinderPlus & database verion**
Click to see AMRFinderplus v3.11.4 and older versions!
| [https://github.com/ncbi/amr](https://github.com/ncbi/amr) | | [NCBI table2asn](https://hub.docker.com/r/staphb/ncbi-table2asn)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-table2asn)](https://hub.docker.com/r/staphb/ncbi-table2asn) | | [https://www.ncbi.nlm.nih.gov/genbank/table2asn/](https://www.ncbi.nlm.nih.gov/genbank/table2asn/)
[https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/](https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/) | +| [ONTime](https://hub.docker.com/r/staphb/ontime)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ontime)](https://hub.docker.com/r/staphb/ontime) | | https://github.com/mbhall88/ontime | | [OrthoFinder](https://hub.docker.com/r/staphb/OrthoFinder)
[![docker pulls](https://badgen.net/docker/pulls/staphb/orthofinder)](https://hub.docker.com/r/staphb/orthofinder) | | https://github.com/davidemms/OrthoFinder | | [Panaroo](https://hub.docker.com/r/staphb/panaroo)
[![docker pulls](https://badgen.net/docker/pulls/staphb/panaroo)](https://hub.docker.com/r/staphb/panaroo) | | https://github.com/gtonkinhill/panaroo | | [Pangolin](https://hub.docker.com/r/staphb/pangolin)
[![docker pulls](https://badgen.net/docker/pulls/staphb/pangolin)](https://hub.docker.com/r/staphb/pangolin) |
Click to see Pangolin v4.2 and older versions! **Pangolin version & pangoLEARN data release date** **Pangolin version & pangolin-data version**
**Pangolin version & pangolin-data version** | https://github.com/cov-lineages/pangolin
https://github.com/cov-lineages/pangoLEARN
https://github.com/cov-lineages/pango-designation
https://github.com/cov-lineages/scorpio
https://github.com/cov-lineages/constellations
https://github.com/cov-lineages/lineages (archived)
https://github.com/hCoV-2019/pangolin (archived) | diff --git a/ontime/0.2.3/Dockerfile b/ontime/0.2.3/Dockerfile new file mode 100644 index 000000000..b1c40ae8b --- /dev/null +++ b/ontime/0.2.3/Dockerfile @@ -0,0 +1,70 @@ +ARG ONTIME_VER="0.2.3" +ARG TARGET="x86_64-unknown-linux-musl" + +FROM rust:1.70 AS builder + +ARG ONTIME_VER +ARG TARGET + +RUN apt update \ + && apt install -y musl-tools + +RUN wget -q https://github.com/mbhall88/ontime/archive/refs/tags/${ONTIME_VER}.tar.gz && \ + tar zxf ${ONTIME_VER}.tar.gz && \ + rm ${ONTIME_VER}.tar.gz && \ + ls / && \ + cd /ontime-${ONTIME_VER} && \ + rustup target add "${TARGET}" && \ + cargo build --release --target "${TARGET}" && \ + strip target/${TARGET}/release/ontime + +FROM ubuntu:jammy as app + +ARG ONTIME_VER +ARG TARGET + +# 'LABEL' instructions tag the image with metadata that might be important to the user +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="ontime" +LABEL software.version="${ONTIME_VER}" +LABEL description="Filters nanopore reads by time" +LABEL website="https://github.com/mbhall88/ontime" +LABEL license="https://github.com/mbhall88/ontime/blob/main/LICENSE" +LABEL maintainer="Erin Young" +LABEL maintainer.email="eriny@utah.gov" + +COPY --from=builder /ontime-${ONTIME_VER}/target/${TARGET}/release/ontime /bin/ + +# for playing nice with workflow managers +RUN apt-get update && apt-get install -y --no-install-recommends \ + ca-certificates \ + procps && \ + apt-get autoclean && \ + rm -rf /var/lib/apt/lists/* + +ENV PATH="$PATH" \ + LC_ALL=C + +# 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.' +CMD ontime --help + +# 'WORKDIR' sets working directory +WORKDIR /data + +# A second FROM insruction creates a new stage +# The test stage must be downstream from 'app' +FROM app as test + +# set working directory so that all test inputs & outputs are kept in /test +WORKDIR /test + +# print help and version info; check dependencies (not all software has these options available) +# Mostly this ensures the tool of choice is in path and is executable +RUN ontime --help && \ + ontime --version + +COPY tests/test.fastq.gz . + +RUN ontime --to 1h test.fastq.gz -o ontime.test.txt && \ + head ontime.test.txt \ No newline at end of file diff --git a/ontime/0.2.3/README.md b/ontime/0.2.3/README.md new file mode 100644 index 000000000..1ed35bf95 --- /dev/null +++ b/ontime/0.2.3/README.md @@ -0,0 +1,28 @@ +# ontime container + +Main tool: [ONTime](https://github.com/mbhall88/ontime/tree/main) + +Code repository: https://github.com/mbhall88/ontime + +Basic information on how to use this tool: +- executable: ontime +- help: --help +- version: --version +- description: Extracts nanopore reads based on when in the run reads were generated. + +Full documentation: https://github.com/mbhall88/ontime/tree/main + +WARNING : the nanopore fastq file MUST still have the time stamp on the reads in the fastq fime, so this tool is **NOT** expected to run on reads downloaded from public repositories. + +## Example Usage + +```bash +# reads from the first five hours +ontime --to 5h in.fq +# reads after the first 24 hours +ontime --from 24h in.fq +# Check what the earliest and latest start times in the fastq are +ontime --show in.fq +``` + + \ No newline at end of file diff --git a/ontime/0.2.3/tests/test.fastq.gz b/ontime/0.2.3/tests/test.fastq.gz new file mode 100755 index 000000000..6121038a0 Binary files /dev/null and b/ontime/0.2.3/tests/test.fastq.gz differ