Add dependencies for GenoFLU

Add dependencies for GenoFLU to run in avian-flu:
- makeblastdb (from NCBI BLAST)
- blastn (from NCBI BLAST)
- openpyxl (for pandas.read_excel)

Resolves <#242>

Author: joverlee521

Dockerfile

@@ -158,6 +158,12 @@ RUN curl -L https://github.com/shenwei356/csvtk/releases/download/v0.30.0/csvtk_
 # Download seqkit
 RUN curl -L https://github.com/shenwei356/seqkit/releases/download/v2.2.0/seqkit_${TARGETOS}_${TARGETARCH}.tar.gz | tar xz --no-same-owner -C /final/bin
 
+# Download ncbi-blast+
+# Only keeping makeblastdb and blastn since that's all we need for Geno-FLU
+RUN curl -L -o ncbi-blast.tar.gz https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.16.0/ncbi-blast-2.16.0+-$(/builder-scripts/target-arch-alternative)-${TARGETOS}.tar.gz \
+ && tar -x --no-same-owner -C /final/bin -z --strip-components 2 --wildcards -f ncbi-blast.tar.gz "*/bin/makeblastdb" "*/bin/blastn" \
+ && rm -f ncbi-blast.tar.gz
+
 # 3. Add unpinned programs
 
 # Allow caching to be avoided from here on out in this stage by calling
@@ -259,6 +265,9 @@ RUN pip3 install pango_aliasor==0.3.0
 RUN pip3 install pathogen-embed==3.0.0
 RUN pip3 install xlrd==2.0.1
 
+# Install openpyxl for pandas in GenoFLU
+RUN pip3 install openpyxl==3.1.0
+
 # 2. Add unpinned programs
 
 # Allow caching to be avoided from here on out in this stage by calling