optimOTU 5.1

Author: METS0JA

image_development/Dockerfile_optimOTU2 renamed to image_development/Dockerfile_optimOTU

@@ -1,13 +1,22 @@
-FROM --platform=linux/amd64 ubuntu:24.04
+FROM ubuntu:24.04
 ENV LANG=C.UTF-8
 ENV LC_ALL=C.UTF-8
 ENV CONDA_DIR=/opt/conda
 ENV PATH=$CONDA_DIR/bin:$PATH
 RUN apt-get update && \
-    apt-get install -y wget git zip build-essential zlib1g-dev && \
-    git clone --branch main https://github.com/brendanf/optimotu_targets.git /optimotu_targets
-COPY image_development/protaxFungi/ /optimotu_targets/protaxFungi/
-COPY image_development/protaxAnimal/ /optimotu_targets/protaxAnimal/
+    apt-get install -y wget git zip unzip build-essential zlib1g-dev && \
+    wget -O /tmp/optimotu_targets.zip https://github.com/brendanf/optimotu_targets/archive/refs/tags/v5.1.0.zip && \
+    unzip /tmp/optimotu_targets.zip -d /tmp && \
+    mv /tmp/optimotu_targets-5.1.0 /optimotu_targets
+# Download protax assets instead of copying from build context
+RUN cd /optimotu_targets && \
+    rm -rf /optimotu_targets/protaxFungi && \
+    wget -O /optimotu_targets/protaxFungi.zip https://nextcloud.jyu.fi/index.php/s/JCdqdNPgsNqJw6o/download && \
+    unzip /optimotu_targets/protaxFungi.zip -d /optimotu_targets && \
+    rm /optimotu_targets/protaxFungi.zip && \
+    wget -O /optimotu_targets/protaxAnimal.zip https://nextcloud.jyu.fi/index.php/s/74p3zTjRjLX76fb/download && \
+    unzip /optimotu_targets/protaxAnimal.zip -d /optimotu_targets && \
+    rm /optimotu_targets/protaxAnimal.zip
 COPY image_development/OptimOTU_v5.yaml /
 
 RUN sed -i 's|BASEDIR=$(pwd)|BASEDIR="/optimotu_targets"|g' /optimotu_targets/scripts/runprotax && \
@@ -30,6 +39,8 @@ RUN sed -i 's|BASEDIR=$(pwd)|BASEDIR="/optimotu_targets"|g' /optimotu_targets/sc
     cd /optimotu_targets && \
     wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
     /bin/bash ~/miniconda.sh -b -p /opt/conda && \
+    conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main && \
+    conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r && \
     conda env create -f /OptimOTU_v5.yaml && \
     chmod -R 777 /opt/conda/envs/OptimOTU_v5 && \
     eval "$(conda shell.bash hook)" && \
@@ -43,13 +54,15 @@ RUN sed -i 's|BASEDIR=$(pwd)|BASEDIR="/optimotu_targets"|g' /optimotu_targets/sc
     usearch -makeudb_usearch protaxFungi/addedmodel/sintaxits2.fasta -output protaxFungi/addedmodel/sintaxits2.udb && \
     usearch -makeudb_usearch protaxFungi/addedmodel/amptk_synmock.fasta -output protaxFungi/addedmodel/amptk_synmock.udb && \
     usearch -makeudb_usearch protaxFungi/addedmodel/its2.fa -output protaxFungi/addedmodel/its2.udb && \
+    sed -i "s/usearch10.0.240_i86linux32/usearch/" /optimotu_targets/scripts/102_protax_refseqs.R && \
     rm -f /optimotu_targets/5dcbe93a-b50c-4ff5-8898-528160c4e593.zip && \
     rm -f /optimotu_targets/FinPROTAX.zip && \
     rm -f /optimotu_targets/protaxAnimal_bin.zip && \
     rm -f ~/miniconda.sh && \
+    rm -f /tmp/optimotu_targets.zip && \
     rm -rf /optimotu_targets/protaxAnimal_bin && \
     conda clean -afy && \
-    apt-get remove -y wget git build-essential && \
+    apt-get remove -y wget git zip unzip build-essential && \
     apt-get autoremove -y && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/* && \

src/components/Run.vue

@@ -907,7 +907,7 @@ export default {
           await this.$store.dispatch('clearContainerConflicts', 'optimotu');
           try {            
             const container = await this.$docker.createContainer({
-              Image: 'pipecraft/optimotu:5',
+              Image: 'pipecraft/optimotu:5.1',
               name: 'optimotu',
               Cmd: ['/scripts/run_optimotu.sh'],
               Tty: true,