update to docker nmdc_taxa_profilers:1.0.5

Dockerfile

@@ -2,35 +2,44 @@ FROM continuumio/miniconda3:latest
 
 LABEL developer="Po-E Li"
 LABEL email="[email protected]"
-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

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: "[email protected]"
-        version: "1.0.4"
+        version: "1.0.5"
     }
 }
 

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"
     }
-}
+}