Snakemake pipeline fixes and downstream data updates from PR #166

- Replace dedent/cd/wget pattern with curl --create-dirs throughout Snakefile
  to fix silent failures where shell sections would exit without running commands
- Update Ensembl download to use may2025.archive.ensembl.org (main site broken)
  and move query string to download_ensembl_curl_config.txt
- Update CGI biomarkers download URL (changed upstream, no longer zipped)
- Add Dockerfile.snakemake: multi-stage build with npm rebuild to fix Node
  version compilation issues with native deps (node-expat/xml-stream)
- Add downloadCosmic.sh helper script for COSMIC download auth flow
- Fix fdaSrs/index.js: UNII file header renamed 'PT' -> 'Display Name' upstream,
  causing all 168k records to be skipped silently
- Update data/signatures.json: add sourceIdVersion '3' to all COSMIC signatures
  (DBS/ID/SBS series) and add name field for proper versioned record lookup

Co-authored-by: Matthew Stuart-Edwards <m.stuartedwards@uleth.ca>

Author: elewis2

Dockerfile.snakemake

@@ -0,0 +1,46 @@
+FROM node:18 AS node_stage
+WORKDIR /usr/src/app
+# Bundle app source
+COPY package*.json ./
+RUN rm -rf node_modules
+RUN npm install
+RUN npm ci --only=production
+# COPY everything not in dockerignore file
+COPY . .
+# set to avoid errors when singularity overloads working dir
+ENV NODE_PATH=/usr/src/app/node_modules
+
+FROM ubuntu:noble
+WORKDIR /usr/src/app
+COPY --from=node_stage /usr/src/app/package*.json ./
+COPY --from=node_stage /usr/src/app/node_modules ./node_modules
+
+RUN apt-get update && \
+    apt-get install -y curl && \
+    curl -fsSL https://deb.nodesource.com/setup_16.x | bash - && \
+    apt-get install -y nodejs python3 python3-pip python3-pulp python3-wheel snakemake unzip wget nano
+
+# Verify Node.js version
+RUN node -v
+
+#RUN pip3 install --upgrade setuptools pip wheel && \
+    #pip3 install "pulp<2.3.1" && \
+    #pip3 install snakemake
+
+RUN mkdir /usr/src/app/snakemake_data
+RUN mkdir /usr/src/app/snakemake_logs
+RUN chmod 777 /usr/src/app/snakemake_data
+RUN chmod 777 /usr/src/app/snakemake_logs
+
+# Copy the Snakefile to the working directory (assuming it's already in the build context)
+COPY . .
+COPY ./download_ensembl_curl_config.txt /usr/src/app/
+COPY ./downloadCosmic.sh /usr/src/app
+
+# Still getting NODE version errors, but a rebuild is quick and helps.
+RUN npm rebuild
+
+# Run the Snakefile using Snakemake
+#CMD [ "sh", "-c", "snakemake --debug -j 1 --config gkb_url=$GKB_URL gkb_user=$GKB_USER gkb_pass=$GKB_PASS --until $GKB_LOADER"]
+CMD [ "sh", "-c", "snakemake --debug -j 1 --config gkb_url=$GKB_URL gkb_user=$GKB_USER gkb_pass=$GKB_PASS"]
+