diff --git a/Dockerfile b/Dockerfile index ed38887..e55d571 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,35 +2,44 @@ FROM continuumio/miniconda3:latest LABEL developer="Po-E Li" LABEL email="po-e@lanl.gov" -LABEL version="1.0.4" +LABEL version="1.0.5" LABEL software="nmdc_taxa_profilers" LABEL tags="metagenome, bioinformatics, NMDC, taxonomy" ENV container docker -RUN apt-get update -y \ - && apt-get install -y build-essential unzip wget curl gawk \ +# system updates +RUN apt-get update --allow-releaseinfo-change \ + && apt-get install -y build-essential \ && apt-get clean # add conda channels RUN conda config --add channels conda-forge \ && conda config --add channels bioconda +# install singlem +RUN wget https://github.com/wwood/singlem/archive/refs/tags/v0.15.0.tar.gz \ + && tar -xzf v0.15.0.tar.gz +RUN conda env create -n singlem -f singlem-0.15.0/singlem.yml \ + && ln -s ${PWD}/singlem-0.15.0/bin/* /opt/conda/envs/singlem/bin/ +RUN rm -f v0.15.0.tar.gz + # install gottcha2 -RUN conda install minimap2 pandas -RUN wget https://github.com/poeli/GOTTCHA2/archive/2.1.8.1.tar.gz \ - && tar -xzf 2.1.8.1.tar.gz \ - && cp GOTTCHA2-2.1.8.1/*.py /usr/local/bin \ - && rm -rf GOTTCHA2-2.1.8.1/ 2.1.8.1.zip +RUN wget https://github.com/poeli/GOTTCHA2/archive/refs/tags/2.1.8.5.tar.gz \ + && tar -xzf 2.1.8.5.tar.gz +RUN conda env create -n gottcha2 -f GOTTCHA2-2.1.8.5/environment.yml \ + && cp GOTTCHA2-2.1.8.5/gottcha/scripts/*.py /usr/local/bin +RUN rm -rf GOTTCHA2-2.1.8.5/ 2.1.8.5.tar.gz # install kraken2 -RUN conda install kraken2=2.1.2 +RUN conda create -n kraken2 kraken2=2.1.2 # install centrifuge RUN conda create -n centrifuge centrifuge=1.0.4_beta # install krona -RUN conda install krona \ +# The "curl" +RUN conda install curl krona \ && ktUpdateTaxonomy.sh # install additional libs diff --git a/ReadbasedAnalysis.wdl b/ReadbasedAnalysis.wdl index d6b0a04..7185b76 100644 --- a/ReadbasedAnalysis.wdl +++ b/ReadbasedAnalysis.wdl @@ -13,7 +13,7 @@ workflow ReadbasedAnalysis { String prefix=sub(proj, ":", "_") Boolean? paired = false String bbtools_container="microbiomedata/bbtools:38.96" - String? docker = "microbiomedata/nmdc_taxa_profilers:1.0.4" + String? docker = "microbiomedata/nmdc_taxa_profilers:1.0.5" call stage { input: @@ -105,7 +105,7 @@ workflow ReadbasedAnalysis { meta { author: "Po-E Li, B10, LANL" email: "po-e@lanl.gov" - version: "1.0.4" + version: "1.0.5" } } diff --git a/options.json b/options.json index 58e40ab..7ca1569 100644 --- a/options.json +++ b/options.json @@ -1,5 +1,5 @@ { "default_runtime_attributes": { - "docker": "microbiomedata/nmdc_taxa_profilers:1.0.0" + "docker": "microbiomedata/nmdc_taxa_profilers:1.0.5" } -} \ No newline at end of file +}