Modify mmseqs2 to use pre-built assets and docker conainers

mmseqs2/Dockerfile

@@ -0,0 +1,23 @@
+# Use Ubuntu Jammy as the base image
+FROM ubuntu:jammy
+
+# Define the ARG for the download URL
+ARG MMSEQS_URL=https://dev.mmseqs.com/latest/mmseqs-linux-gpu.tar.gz
+
+# Install necessary packages
+ENV DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && apt-get install -y \
+    wget \
+    tar \
+    && rm -rf /var/lib/apt/lists/*
+
+# Download and extract the mmseqs-linux-avx2.tar.gz file
+RUN wget ${MMSEQS_URL} -O /tmp/mmseqs.tar.gz \
+    && tar -xzf /tmp/mmseqs.tar.gz -C /opt \
+    && rm /tmp/mmseqs.tar.gz
+
+# Add the mmseqs binary to the PATH
+ENV PATH="/opt/mmseqs/bin:${PATH}"
+
+# Default command
+CMD ["mmseqs"]

mmseqs2/avx2/container.yaml

@@ -0,0 +1,15 @@
+docker: jterstriep/mmseqs-linux-avx2
+url: https://github.com/soedinglab/MMseqs2
+maintainer: "@jterstriep"
+
+description: "MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is free and open source software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed."
+
+
+latest:
+  "17-b804f": sha256:4f9e1e64a4f02a70adf8b12814d360276b970a009d502f55b1fbd2b90182b8e2
+tags:
+  "17-b804f": sha256:4f9e1e64a4f02a70adf8b12814d360276b970a009d502f55b1fbd2b90182b8e2
+
+aliases:
+  mmseqs: /opt/mmseqs/bin/mmseqs
+

mmseqs2/avx2/mmseqs2.def

@@ -0,0 +1,24 @@
+Bootstrap: docker
+From: ubuntu:jammy
+
+%post
+    # Update and install necessary packages
+    apt-get update && apt-get install -y wget
+
+    cd /opt
+    wget https://dev.mmseqs.com/latest/mmseqs-linux-avx2.tar.gz
+    tar xzf mmseqs-linux-avx2.tar.gz
+    rm mmseqs-linux-avx2.tar.gz
+
+%environment
+    # Set environment variables
+    export PATH=/opt/mmseqs/bin
+
+%runscript
+    # Define the default command
+    /opt/mmseqs2/build/bin/mmseqs "$@"
+
+%labels
+    Author: Jeff Terstriep
+    Version: 1.0
+    Description: Singularity container for MMseqs2 avx2 version (bindary download)

mmseqs2/container.yaml → mmseqs2/gpu/container.yaml

@@ -1,20 +1,17 @@
-# fake path for locally built container
-path: mmseqs2_gpu.sif
+docker: jterstriep/mmseqs-linux-gpu
 url: https://github.com/soedinglab/MMseqs2
 maintainer: "@jterstriep"
 
 description: "MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is free and open source software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed."
 
 
-# fake hashes for locally built container
 latest:
-  "16-747c6": sha256:caae00cea035b1aba1a9a38e39cecf2ecc7f6ba443187204b405302645e7cac1
+  "17-b804f": sha256:7b2e3e68f3c3fcdf66cb509839ab220abe8c5a67044f97c35a9e3d91bcf07065
 tags:
-  "16-747c6": sha256:caae00cea035b1aba1a9a38e39cecf2ecc7f6ba443187204b405302645e7cac1
+  "17-b804f": sha256:7b2e3e68f3c3fcdf66cb509839ab220abe8c5a67044f97c35a9e3d91bcf07065
 
 aliases:
-  mmseqs: /opt/MMseqs2/build/bin/mmseqs
-  mmseqs_gpu: /opt/MMseqs2/build/bin/mmseqs
+  mmseqs: /opt/mmseqs/bin/mmseqs
 
 features:
   gpu: true

mmseqs2/gpu/mmseqs2-gpu.def

@@ -0,0 +1,24 @@
+Bootstrap: docker
+From: ubuntu:jammy
+
+%post
+    # Update and install necessary packages
+    apt-get update && apt-get install -y wget
+
+    cd /opt
+    wget https://dev.mmseqs.com/latest/mmseqs-linux-gpu.tar.gz
+    tar xzf mmseqs-linux-gpu.tar.gz
+    rm mmseqs-linux-gpu.tar.gz
+
+%environment
+    # Set environment variables
+    export PATH=/opt/mmseqs/bin
+
+%runscript
+    # Define the default command
+    /opt/mmseqs2/build/bin/mmseqs "$@"
+
+%labels
+    Author: Jeff Terstriep
+    Version: 1.0
+    Description: Singularity container for MMseqs2 PU version (binary download)