Merge pull request #334 from Ensembl/lcampbell/assembly_status

Addition of a new sub-module 'status' to assembly module.

containers/ncbi_datasets_v16.10.0.def

@@ -0,0 +1,65 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+Bootstrap: docker
+From: ubuntu:24.04
+
+%environment
+    export SINGULARITY_SHELL=/bin/bash
+    export DEBIAN_FRONTEND=noninteractive
+    export LC_ALL=C
+
+%labels
+    Author ensembl-metazoa@ebi.ac.uk
+    Software "NCBI's datasets and dataformat"
+    Software.version v16.10.0
+    Software.website "https://github.com/ncbi/datasets/releases/tag/v16.10.0"
+    Description "NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases."
+
+%post
+    apt-get update && apt-get -y upgrade
+    apt-get -y install \
+    wget \
+    unzip \
+    procps \
+    ca-certificates \
+
+    rm -rf /var/lib/apt/lists/*
+    apt-get clean
+
+    #Installing ncbi datasets & dataformat
+    cd /usr/local/bin/ && \
+    wget https://github.com/ncbi/datasets/releases/download/v16.10.0/linux-amd64.cli.package.zip && \
+    unzip linux-amd64.cli.package.zip && \
+    rm linux-amd64.cli.package.zip && \
+    chmod +x datasets dataformat
+
+%test
+    #!/usr/bin/bash
+    echo "Testing OS is Ubuntu...."
+    source /etc/os-release
+    grep -q -e "PRETTY_NAME=\"Ubuntu" /etc/os-release
+    if [ $? -eq 0 ]; then
+        if [ $VERSION_ID == "24.04" ]; then
+	   echo "Container base is Ubuntu version ${VERSION_ID} as expected."
+        fi
+    else
+        echo "Container base is not Ubuntu."
+        exit 1
+    fi
+
+    echo -e -n "\n** Checking we have datasets installed **\n"
+    datasets --version
+    datasets --help

pyproject.toml

@@ -55,6 +55,7 @@ dependencies = [
     "mysql-connector-python >= 8.0.29",
     "python-redmine >= 2.3.0",
     "requests >= 2.28.0",
+    "spython >= 0.3.13",
 ]
 
 [project.optional-dependencies]
@@ -91,6 +92,7 @@ documentation = "https://ensembl.github.io/ensembl-genomio"
 [project.scripts]
 # Assembly
 assembly_download = "ensembl.io.genomio.assembly.download:main"
+assembly_tracker = "ensembl.io.genomio.assembly.status:main"
 # Database
 database_factory = "ensembl.io.genomio.database.factory:main"
 # Events

src/python/ensembl/io/genomio/assembly/__init__.py

@@ -15,3 +15,4 @@
 """Assembly preparation module."""
 
 from .download import *
+from .status import *