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tbprofiler v6.4.1 #1108

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Nov 21, 2024
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50ccd8b
add genoflu
sage-wright Jul 10, 2024
c7436d8
add readme
sage-wright Jul 10, 2024
974d6e1
add to license
sage-wright Jul 10, 2024
bef89c2
add --force-pkgs-dirs
sage-wright Jul 11, 2024
fd3397e
Merge branch 'StaPH-B:master' into main
sage-wright Sep 23, 2024
79ad63e
Merge branch 'StaPH-B:master' into main
sage-wright Oct 10, 2024
7fc8de3
krakentools add
sage-wright Oct 10, 2024
4327e5d
update readmes
sage-wright Oct 10, 2024
25cd73a
silence warnings about AS casing; fix typo
kapsakcj Oct 22, 2024
da6080d
added comment in dockerfile & added additional dependencies and versi…
kapsakcj Oct 22, 2024
f4b3565
pinning biopython and pandas versions and removing unnecessary jq and…
kapsakcj Oct 23, 2024
3eb82ab
fixed version of python installed listed in krakentools readme
kapsakcj Oct 23, 2024
f2db335
Merge branch 'StaPH-B:master' into main
sage-wright Oct 31, 2024
570fccb
add tbprofiler 6.4.0
sage-wright Oct 31, 2024
39777c4
Merge branch 'main' of https://github.com/sage-wright/docker-builds i…
sage-wright Oct 31, 2024
f650fcb
update readme
sage-wright Oct 31, 2024
b6837a0
add list_db
sage-wright Oct 31, 2024
245b7b6
exec format, capitalize AS
sage-wright Oct 31, 2024
c1cd8c6
update versions
sage-wright Oct 31, 2024
8ed51f3
pinning delly version due to conflict resolution with usher 0.6.3 whi…
kapsakcj Nov 1, 2024
1e90eaf
added delly to list of deps for tb-profiler. Plus link to GH issue de…
kapsakcj Nov 1, 2024
107e463
Merge branch 'StaPH-B:master' into main
sage-wright Nov 20, 2024
e195bf7
add 6.4.1
sage-wright Nov 20, 2024
a35ae1b
update readme
sage-wright Nov 20, 2024
be5eb60
correct versions of a few dependencies in tbprofiler readme
kapsakcj Nov 20, 2024
094ea4f
Update Dockerfile
sage-wright Nov 21, 2024
4b5fef9
Update README.md
sage-wright Nov 21, 2024
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add genoflu
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sage-wright committed Jul 10, 2024
commit 50ccd8ba456a0b16b00522bacdb72153743fdfa0
51 changes: 51 additions & 0 deletions genoflu/1.0.3/Dockerfile
Original file line number Diff line number Diff line change
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FROM mambaorg/micromamba:1.5.8 as app

USER root
WORKDIR /

ARG GENOFLU_VER="1.0.3"

# LABEL instructions tag the image with metadata that might be important to the user
LABEL base.image="micromamba:1.5.8"
LABEL dockerfile.version="1"
LABEL software="genoflu"
LABEL software.version=$GENOFLU_VER
LABEL description="Uses BLAST to detect whole-genome flu genotype"
LABEL website="https://github.com/USDA-VS/GenoFLU"
LABEL license="https://github.com/USDA-VS/GenoFLU/blob/main/LICENSE"
LABEL maintainer="Sage Wright"
LABEL maintainer.email="[email protected]"

# Install dependencies via apt-get; cleanup apt garbage
RUN apt-get update && apt-get install -y --no-install-recommends \
wget \
ca-certificates \
procps && \
apt-get autoclean && rm -rf /var/lib/apt/lists/*

# install genoflu via bioconda; install into 'base' conda env
RUN micromamba install --yes --name base --channel conda-forge --channel bioconda \
genoflu=${GENOFLU_VER} && \
micromamba clean --all --yes


# ENV instructions set environment variables that persist from the build into the resulting image
# hardcode 'base' env bin into PATH, so conda env does not have to be "activated" at run time
ENV PATH="/opt/conda/bin:${PATH}"

# WORKDIR sets working directory
WORKDIR /data

# default command is to pull up help options for genoflu
CMD [ "genoflu.py", "--help" ]

# A second FROM insruction creates a new stage
# We use `test` for the test image
FROM app as test

# getting all the exectubles in bin
RUN genoflu.py --help && genoflu.py --version

# testing a genome
RUN wget -q https://raw.githubusercontent.com/USDA-VS/GenoFLU/main/test/test-genome-A1.fasta && \
genoflu.py -f test-genome-A1.fasta