Merge pull request #4 from rroutsong/install_metwrap

Install metawrap
OpenOmics · Aug 16, 2023 · f6d15bc · f6d15bc
2 parents 30e6011 + ef14f3e
commit f6d15bc
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diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -1,4 +1,3 @@
-ARG ENV_CONTEXT=metagenome
 FROM mambaorg/micromamba 
 # $MAMBA_USER from inherited image
 
@@ -13,6 +12,12 @@ USER $MAMBA_USER
 
 # setup up metagenome environment
 COPY assets /assets
+ENV ENV_NAME=metagenome
 RUN micromamba create -f /assets/base.yaml
-RUN micromamba create -f /assets/metawrap.yaml
-ENV ENV_NAME=$ENV_CONTEXT
+
+# setup metawrap environment
+RUN micromamba create -n metawrap_env
+RUN micromamba install -y --only-deps -n metawrap_env -c defaults -c conda-forge -c bioconda -c ursky metawrap-mg
+RUN micromamba install -y -n metawrap_env -c ursky metawrap-mg=1.3.2
+RUN micromamba install -y -n metawrap_env -c defaults -c conda-forge -c bioconda -c ursky biopython blas=2.5 blast=2.6.0 bmtagger bowtie2 bwa checkm-genome fastqc kraken=1.1 kraken2 krona=2.7 matplotlib maxbin2 megahit metabat2 pandas prokka quast r-ggplot2 r-recommended salmon samtools=1.9 seaborn spades trim-galore
+RUN micromamba install -y -n metawrap_env -c ursky concoct=1.0.0 pplacer
diff --git a/docker/assets/base.yaml b/docker/assets/base.yaml
@@ -10,4 +10,4 @@ dependencies:
   - bbmap==38.87
   - humann==3.0.0
   - gunc==1.0.5
-  - GTDBtk==2.1.1
+  - GTDBtk==2.1.1
diff --git a/docker/assets/metawrap.yaml b/docker/assets/metawrap.yaml