Create assembly, add webin-cli to docker container, add call to API t…

…o check status of assembly submission.

ena-submission/Dockerfile

@@ -1,5 +1,14 @@
 FROM mambaorg/micromamba:1.5.8
 
+# Install dependencies needed for webin-cli
+USER root
+RUN apt-get update && apt-get install -y \
+    default-jre \
+    wget \
+    && rm -rf /var/lib/apt/lists/*
+RUN mkdir -p /package
+USER $MAMBA_USER
+
 COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/env.yaml
 COPY --chown=$MAMBA_USER:$MAMBA_USER .mambarc /tmp/.mambarc
 
@@ -10,6 +19,11 @@ RUN micromamba config set extract_threads 1 \
 # Set the environment variable to activate the conda environment
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
-COPY --chown=$MAMBA_USER:$MAMBA_USER . /package
 
+ENV WEBIN_CLI_VERSION 7.3.1
+USER root
+RUN wget -q "https://github.com/enasequence/webin-cli/releases/download/${WEBIN_CLI_VERSION}/webin-cli-${WEBIN_CLI_VERSION}.jar" -O /package/webin-cli.jar
+USER $MAMBA_USER
+
+COPY --chown=$MAMBA_USER:$MAMBA_USER . /package
 WORKDIR /package

ena-submission/ENA_submission.md

@@ -277,7 +277,34 @@ The following could be implement as post-MVP features:
        -password YYYYYY
    ```
 
-5. Save accession numbers (these will be returned by the webin-cli)
+5. Save ERZ accession numbers (these will be returned by the webin-cli)
+6. Wait to receive GCA accession numbers (returned later after assignment by NCBI). This can be retrieved via https://wwwdev.ebi.ac.uk/ena/submit/report/swagger-ui/index.html
+
+```
+curl -X 'GET' \
+  'https://www.ebi.ac.uk/ena/submit/report/analysis-process/{erz_accession}?format=json&max-results=100' \
+  -H 'accept: */*' \
+  -H 'Authorization: Basic KEY'
+```
+
+When processing is finished the response should look like:
+
+```
+[
+  {
+    "report": {
+      "id": "{erz_accession}",
+      "analysisType": "SEQUENCE_ASSEMBLY",
+      "acc": "chromosomes:OZ076380-OZ076381,genome:GCA_964187725.1",
+      "processingStatus": "COMPLETED",
+      "processingStart": "14-06-2024 05:07:40",
+      "processingEnd": "14-06-2024 05:08:19",
+      "processingError": null
+    },
+    "links": []
+  }
+]
+```
 
 ## Promises made to ENA
 

ena-submission/README.md

@@ -44,4 +44,10 @@ micromamba create -f environment.yml --platform osx-64 --rc-file .mambarc
 micromamba activate loculus-ena-submission
 ```
 
+In order to submit assemblies you will also need to install ENA's `webin-cli.jar`. Their [webpage](https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html) offers more instructions. This pipeline has been tested with `WEBIN_CLI_VERSION=7.3.1`.
+
+```bash
+ wget -q "https://github.com/enasequence/webin-cli/releases/download/${WEBIN_CLI_VERSION}/webin-cli-${WEBIN_CLI_VERSION}.jar" -O /package/webin-cli.jar
+```
+
 Then run snakemake using `snakemake` or `snakemake {rule}`.

ena-submission/Snakefile

@@ -119,6 +119,21 @@ rule create_sample:
         sample_created=touch("results/sample_created"),
     params:
         log_level=LOG_LEVEL,
+    shell:
+        """
+        python {input.script} \
+            --config-file {input.config} \
+            --log-level {params.log_level} \
+        """
+
+rule create_assembly:
+    input:
+        script="scripts/create_assembly.py",
+        config="results/config.yaml",
+    output:
+        sample_created=touch("results/assembly_created"),
+    params:
+        log_level=LOG_LEVEL,
     shell:
         """
         python {input.script} \

ena-submission/config/defaults.yaml

@@ -10,6 +10,7 @@ ena_submission_url: https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit
 github_username: fake_username
 github_pat: fake_pat
 github_url: https://api.github.com/repos/pathoplexus/ena-submission/contents/test/approved_ena_submission_list.json?ref=main
+ena_reports_service_url: https://wwwdev.ebi.ac.uk/ena/submit/report
 metadata_mapping:
   'subject exposure':
     loculus_fields: [exposure_event]