Removing unused dependecies and adding taxonkit

docker/metavirs/Dockerfile

@@ -18,8 +18,7 @@ FROM ubuntu:20.04
 #  - seqtk/1.3            # apt-get, deafult: 1.3
 #  - spades/3.15.4        # from src, installed: 3.15.4
 #  - ucsc/418             # personal mirror: snapshot Nov 2nd, 2020
-#  - blastn/2.13.0+       # download binary, installed: 2.13.0+
-#  - fastx_toolkit/0.0.13 # download binary, installed: 0.0.13
+#  - taxonkit/0.18.0      # download binary, installed: 0.18.0
 LABEL [email protected]
 
 ############### INIT ################
@@ -230,34 +229,26 @@ WORKDIR /opt2
 
 # Install spades/3.15.4 manually, latest version
 # not available to apt-get on Ubuntu/20.04.
-# Dependencies already satisfied:
-RUN wget http://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4-Linux.tar.gz \
+# Not longer available at http://cab.spbu.ru,
+# must be downloaded from Github release.
+# Dependencies already satisfied.
+RUN wget https://github.com/ablab/spades/releases/download/v3.15.4/SPAdes-3.15.4-Linux.tar.gz \
         && tar -xvzf SPAdes-3.15.4-Linux.tar.gz  \
         && rm /opt2/SPAdes-3.15.4-Linux.tar.gz 
 # Add metaspades to $PATH
 ENV PATH="/opt2/SPAdes-3.15.4-Linux/bin:$PATH"
 WORKDIR /opt2
 
-# Install blastn/2.13.0+ from NCBI FTP,
-# not available to apt-get on Ubuntu/20.04.
-# Dependencies already satisfied:
-RUN wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.13.0+-x64-linux.tar.gz \
-        && tar -zvxf ncbi-blast-2.13.0+-x64-linux.tar.gz ./ncbi-blast-2.13.0+/bin/blastn \
-        && rm ncbi-blast-2.13.0+-x64-linux.tar.gz
-# Add blastn to $PATH
-ENV PATH="/opt2/ncbi-blast-2.13.0+/bin:$PATH"
-WORKDIR /opt2
-
-# Install fastx_toolkit/0.0.13 from CSHL,
+# Install taxonkit/0.18.0
 # not available to apt-get on Ubuntu/20.04.
-# Dependencies already satisfied:
-RUN mkdir fastx_toolkit \
-        && cd fastx_toolkit \
-        && wget http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2 \
-        && tar -jvxf fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2 ./bin/fastq_to_fasta \
-        && rm fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2
-# Add fastq_to_fasta to $PATH
-ENV PATH="/opt2/fastx_toolkit/bin:$PATH"
+# Dependencies already satisfied
+RUN mkdir taxonkit-0.18.0 \
+        && cd taxonkit-0.18.0 \
+        && wget https://github.com/shenwei356/taxonkit/releases/download/v0.18.0/taxonkit_linux_amd64.tar.gz \
+        && tar -zvxf taxonkit_linux_amd64.tar.gz \
+        && rm taxonkit_linux_amd64.tar.gz
+# Add taxonkit to $PATH
+ENV PATH="/opt2/taxonkit-0.18.0:$PATH"
 WORKDIR /opt2
 
 ################ POST #################