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adding ontime version 0.3.1 (#906)
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* adding ontime version 0.3.1

* Updated base and added apt-get wget

* Redid test for file extension
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erinyoung authored Mar 20, 2024
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -208,7 +208,7 @@ 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) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-datasets)](https://hub.docker.com/r/staphb/ncbi-datasets) | <details><summary> Click to see all datasets versions </summary> **datasets versions** <ul><li>[13.31.0](./ncbi-datasets/13.31.0/)</li><li>[13.35.0](./ncbi-datasets/13.35.0/)</li><li>[13.43.2](./ncbi-datasets/13.43.2/)</li><li>[14.0.0](./ncbi-datasets/14.0.0/)</li><li>[14.3.0](./ncbi-datasets/14.3.0/)</li><li>[14.7.0](./ncbi-datasets/14.7.0/)</li><li>[14.13.2](./ncbi-datasets/14.13.2/)</li><li>[14.20.0](./ncbi-datasets/14.20.0/)</li><li>[14.27.0](ncbi-datasets/14.27.0/)</li><li>[15.1.0](ncbi-datasets/15.1.0/)</li><li>[15.2.0](ncbi-datasets/15.2.0/)</li><li>[15.11.0](ncbi-datasets/15.11.0/)</li><li>[15.27.1](ncbi-datasets/15.27.1/)</li><li>[15.31.0](ncbi-datasets/15.31.1/)</li><li>[16.2.0](ncbi-datasets/16.2.0/)</li>[16.8.1](./ncbi-datasets/16.8.1/)</ul> | [https://github.com/ncbi/datasets](https://github.com/ncbi/datasets) <br/>[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) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-amrfinderplus)](https://hub.docker.com/r/staphb/ncbi-amrfinderplus) | **AMRFinderPlus & database verion** <details><summary> Click to see AMRFinderplus v3.11.4 and older versions! </summary> <ul><li>3.1.1b</li><li>3.8.4</li><li>3.8.28</li><li>3.9.3</li><li>3.9.8</li><li>3.10.1</li><li>3.10.5</li><li>3.10.16</li><li>3.10.20</li><li>3.10.24</li><li>3.10.30</li><li>3.10.36</li><li>3.10.42</li><li>3.11.2 & 2022-12-19.1</li><li>[3.11.2 & 2023-02-23.1](ncbi-amrfinderplus/3.11.2-2023-02-23.1/)</li><li>[3.11.4 & 2023-02-23.1](ncbi-amrfinderplus/3.11.4-2023-02-23.1/)</li></ul> </details> <ul><li>[3.11.8 & 2023-02-23.1](ncbi-amrfinderplus/3.11.8-2023-02-23.1/)</li><li>[3.11.11 & 2023-04-17.1](ncbi-amrfinderplus/3.11.11-2023-04-17.1)</li><li>[3.11.14 & 2023-04-17.1](ncbi-amrfinderplus/3.11.14-2023-04-17.1/)</li><li>[3.11.17 & 2023-07-13.2](ncbi-amrfinderplus/3.11.17-2023-07-13.2/)</li><li>[3.11.18 & 2023-08-08.2](ncbi-amrfinderplus/3.11.18-2023-08-08.2/)</li><li>[3.11.20 & 2023-09-26.1](ncbi-amrfinderplus/3.11.20-2023-09-26.1/)</li><li>[3.11.26 & 2023-11-15.1](ncbi-amrfinderplus/3.11.26-2023-11-15.1/)</li><li>[3.12.8 & 2024-01-31.1](ncbi-amrfinderplus/3.12.8-2024-01-31.1/)</li></ul> | [https://github.com/ncbi/amr](https://github.com/ncbi/amr) |
| [NCBI table2asn](https://hub.docker.com/r/staphb/ncbi-table2asn) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ncbi-table2asn)](https://hub.docker.com/r/staphb/ncbi-table2asn) | <ul><li>1.26.678</li></ul> | [https://www.ncbi.nlm.nih.gov/genbank/table2asn/](https://www.ncbi.nlm.nih.gov/genbank/table2asn/) <br/>[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) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ontime)](https://hub.docker.com/r/staphb/ontime) | <ul><li>[0.2.3](ontime/0.2.3/)</li></ul> | https://github.com/mbhall88/ontime |
| [ONTime](https://hub.docker.com/r/staphb/ontime) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ontime)](https://hub.docker.com/r/staphb/ontime) | <ul><li>[0.2.3](ontime/0.2.3/)</li><li>[0.3.1](ontime/0.3.1/)</li></ul> | https://github.com/mbhall88/ontime |
| [OrthoFinder](https://hub.docker.com/r/staphb/orthofinder) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/orthofinder)](https://hub.docker.com/r/staphb/orthofinder) | <ul><li>2.17</li></ul> | https://github.com/davidemms/OrthoFinder |
| [Panaroo](https://hub.docker.com/r/staphb/panaroo) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/panaroo)](https://hub.docker.com/r/staphb/panaroo) | <ul><li>[1.2.10](panaroo/1.2.10/)</li><li>[1.3.4](panaroo/1.3.4/)</li></ul>| (https://hub.docker.com/r/staphb/panaroo) |
| [Pangolin](https://hub.docker.com/r/staphb/pangolin) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pangolin)](https://hub.docker.com/r/staphb/pangolin) | <details><summary> Click to see Pangolin v4.2 and older versions! </summary> **Pangolin version & pangoLEARN data release date** <ul><li>1.1.14</li><li>2.0.4 & 2020-07-20</li><li>2.0.5 & 2020-07-20</li><li>2.1.1 & 2020-12-17</li><li>2.1.3 & 2020-12-17</li><li>2.1.6 & 2021-01-06</li><li>2.1.7 & 2021-01-11</li><li>2.1.7 & 2021-01-20</li><li>2.1.8 & 2021-01-22</li><li>2.1.10 & 2021-02-01</li><li>2.1.11 & 2021-02-01</li><li>2.1.11 & 2021-02-05</li><li>2.2.1 & 2021-02-06</li><li>2.2.2 & 2021-02-06</li><li>2.2.2 & 2021-02-11</li><li>2.2.2 & 2021-02-12</li><li>2.3.0 & 2021-02-12</li><li>2.3.0 & 2021-02-18</li><li>2.3.0 & 2021-02-21</li><li>2.3.2 & 2021-02-21</li><li>2.3.3 & 2021-03-16</li><li>2.3.4 & 2021-03-16</li><li>2.3.5 & 2021-03-16</li><li>2.3.6 & 2021-03-16</li><li>2.3.6 & 2021-03-29</li><li>2.3.8 & 2021-04-01</li><li>2.3.8 & 2021-04-14</li><li>2.3.8 & 2021-04-21</li><li>2.3.8 & 2021-04-23</li><li>2.4 & 2021-04-28</li><li>2.4.1 & 2021-04-28</li><li>2.4.2 & 2021-04-28</li><li>2.4.2 & 2021-05-10</li><li>2.4.2 & 2021-05-11</li><li>2.4.2 & 2021-05-19</li><li>3.0.5 & 2021-06-05</li><li>3.1.3 & 2021-06-15</li><li>3.1.5 & 2021-06-15</li><li>3.1.5 & 2021-07-07-2</li><li>3.1.7 & 2021-07-09</li><li>3.1.8 & 2021-07-28</li><li>3.1.10 & 2021-07-28</li><li>3.1.11 & 2021-08-09</li><li>3.1.11 & 2021-08-24</li><li>3.1.11 & 2021-09-17</li><li>3.1.14 & 2021-09-28</li><li>3.1.14 & 2021-10-13</li><li>3.1.16 & 2021-10-18</li><li>3.1.16 & 2021-11-04</li><li>3.1.16 & 2021-11-09</li><li>3.1.16 & 2021-11-18</li><li>3.1.16 & 2021-11-25</li><li>3.1.17 & 2021-11-25</li><li>3.1.17 & 2021-12-06</li><li>3.1.17 & 2022-01-05</li><li>3.1.18 & 2022-01-20</li><li>3.1.19 & 2022-01-20</li><li>3.1.20 & 2022-02-02</li><li>3.1.20 & 2022-02-28</li></ul> **Pangolin version & pangolin-data version** <ul><li>4.0 & 1.2.133</li><li>4.0.1 & 1.2.133</li><li>4.0.2 & 1.2.133</li><li>4.0.3 & 1.2.133</li><li>4.0.4 & 1.2.133</li><li>4.0.5 & 1.3</li><li>4.0.6 & 1.6</li><li>4.0.6 & 1.8</li><li>4.0.6 & 1.9</li><li>4.1.1 & 1.11</li><li>4.1.2 & 1.12</li><li>4.1.2 & 1.13</li><li>4.1.2 & 1.14</li><li>4.1.3 & 1.15.1</li><li>4.1.3 & 1.16</li><li>4.1.3 & 1.17</li><li>4.2 & 1.18</li><li>4.2 & 1.18.1</li><li>4.2 & 1.18.1.1</li><li>4.2 & 1.19</li></ul> </details> **Pangolin version & pangolin-data version** <ul><li>[4.3 & 1.20](pangolin/4.3-pdata-1.20/)</li><li>[4.3 & 1.21](pangolin/4.3-pdata-1.21/)</li><li>[4.3.1 & 1.22](pangolin/4.3.1-pdata-1.22/)</li><li>[4.3.1 & 1.23](pangolin/4.3.1-pdata-1.23/)</li><li>[4.3.1 & 1.23.1](pangolin/4.3.1-pdata-1.23.1/)</li><li>[4.3.1 & 1.23.1 with XDG_CACHE_HOME=/tmp](pangolin/4.3.1-pdata-1.23.1-1/)</li><li>[4.3.1 & 1.24](pangolin/4.3.1-pdata-1.24/)</li><li>[4.3.1 & 1.25.1](pangolin/4.3.1-pdata-1.25.1/)</li><li>[4.3.1 & 1.26](pangolin/4.3.1-pdata-1.26/)</li></ul> | https://github.com/cov-lineages/pangolin<br/>https://github.com/cov-lineages/pangoLEARN<br/>https://github.com/cov-lineages/pango-designation<br/>https://github.com/cov-lineages/scorpio<br/>https://github.com/cov-lineages/constellations<br/>https://github.com/cov-lineages/lineages (archived)<br/>https://github.com/hCoV-2019/pangolin (archived) |
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72 changes: 72 additions & 0 deletions ontime/0.3.1/Dockerfile
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ARG ONTIME_VER="0.3.1"
ARG TARGET="x86_64-unknown-linux-musl"

FROM rust:1.76 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="[email protected]"

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

# testing with files uploaded with prior version
RUN apt-get update && apt-get install -y wget

RUN wget -q https://github.com/StaPH-B/docker-builds/raw/master/ontime/0.2.3/tests/test.fastq.gz && \
ontime --to 1h test.fastq.gz -o ontime.test.fastq.gz && \
ls -alh test.fastq.gz ontime.test.fastq.gz
26 changes: 26 additions & 0 deletions ontime/0.3.1/README.md
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# 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
```

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