-
Notifications
You must be signed in to change notification settings - Fork 125
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #1102 from jessicarowell/master
Update to TOSTADAS v4.0.0 (replaces tbl2asn with table2asn in conda environment.yml file)
- Loading branch information
Showing
3 changed files
with
101 additions
and
1 deletion.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| FROM mambaorg/micromamba:1.5.8 as app | ||
|
|
||
| ARG TOSTADAS_VER="4.0.0" | ||
|
|
||
| USER root | ||
|
|
||
| WORKDIR / | ||
|
|
||
| LABEL authors="Jessica Rowell and Ankush Gupta" | ||
| LABEL base.image="mambaorg/micromamba:1.5.8" | ||
| LABEL dockerfile.version="3" | ||
| LABEL software="tostadas" | ||
| LABEL software.version=$TOSTADAS_VER | ||
| LABEL description="Image for the TOSTADAS: Toolkit for Open Sequence Triage, Annotation and DAtabase Submission pipeline" | ||
| LABEL website="https://github.com/CDCgov/tostadas" | ||
| LABEL license="https://github.com/CDCgov/tostadas/LICENSE" | ||
| LABEL maintainer="Jessica Rowell" | ||
| LABEL maintainer.email="[email protected]" | ||
| LABEL maintainer2="Kyle O'Connell" | ||
| LABEL maintainer2.email="[email protected]" | ||
|
|
||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| wget \ | ||
| ca-certificates \ | ||
| procps && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
|
|
||
| # download tostadas repo, move to /tostadas, and create /data | ||
| RUN wget https://github.com/CDCgov/tostadas/archive/refs/tags/v${TOSTADAS_VER}.tar.gz && \ | ||
| tar -xvf v${TOSTADAS_VER}.tar.gz && \ | ||
| rm v${TOSTADAS_VER}.tar.gz && \ | ||
| mv tostadas-${TOSTADAS_VER} tostadas && \ | ||
| mkdir /data | ||
|
|
||
| # use mamba to install conda packages | ||
| RUN micromamba env create -f tostadas/environment.yml && \ | ||
| micromamba clean -a -y -f && \ | ||
| echo "source activate tostadas" > ~/.bashrc && \ | ||
| rm -rf /tostadas | ||
|
|
||
| ENV PATH=/opt/conda/envs/tostadas/bin:/opt/conda/envs/env/bin:$PATH \ | ||
| LC_ALL=C.UTF-8 | ||
|
|
||
| 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 instruction creates a new stage | ||
| FROM app as test | ||
|
|
||
| RUN liftoff --version && \ | ||
| samtools --version && \ | ||
| python --version && \ | ||
| table2asn -help |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| # tostadas container | ||
|
|
||
| Main tool : [tostadas](https://github.com/CDCgov/tostadas) | ||
| Version: 4.0.0 | ||
|
|
||
| Additional tools installed via conda: | ||
| - pip | ||
| - libgcc-ng=12.1.0=h8d9b700_16 | ||
| - libstdcxx-ng=12.1.0=ha89aaad_16 | ||
| - liftoff=1.6.3=pyhdfd78af_0 | ||
| - lxml=4.9.1=py39hb9d737c_0 | ||
| - nameparser=1.0.5=py_0 | ||
| - numpy=1.22.4=py39hc58783e_0 | ||
| - packaging=21.3=pyhd3eb1b0_0 | ||
| - pandas=1.4.2=py39h1832856_2 | ||
| - paramiko=3.4.0=pyhd8ed1ab_0 | ||
| - python-dateutil=2.8.2=pyhd8ed1ab_0 | ||
| - python_abi=3.9=2_cp39 | ||
| - pytz=2022.1=pyhd8ed1ab_0 | ||
| - pyvcf3=1.0.3=pyhdfd78af_0 | ||
| - pyyaml=6.0=py39hb9d737c_4 | ||
| - readline=8.1=h46c0cb4_0 | ||
| - requests=2.28.0=pyhd8ed1ab_1 | ||
| - samtools=1.15.1=h1170115_0 | ||
| - setuptools=62.3.2=py39hf3d152e_0 | ||
| - simplejson=3.17.6=py39hb9d737c_1 | ||
| - table2asn=1.28.1179=h48fe88c_0 | ||
| - tbb=2021.5.0=h924138e_1 | ||
| - tk=8.6.12=h27826a3_0 | ||
| - tzdata=2022a=h191b570_0 | ||
| - ujson=5.3.0=py39h5a03fae_0 | ||
| - urllib3=1.26.9=pyhd8ed1ab_0 | ||
| - wgs2ncbi=1.1.2=pl5262hdfd78af_1 | ||
| - wheel=0.37.1=pyhd8ed1ab_0 | ||
| - xz=5.2.5=h516909a_1 | ||
| - yaml=0.2.5=h7f98852_2 | ||
| - openpyxl=3.0.10 | ||
| - xmltodict=0.13.0=pyhd8ed1ab_0 | ||
|
|
||
| Full documentation: https://github.com/CDCgov/tostadas | ||
|
|
||
| [tostadas](https://github.com/CDCgov/tostadas) is a Nextflow workflow for annotation and submission of MonkeyPox Virus consensus sequences. The resultant container is not intended to run independently of the workflow. |