Move container related things into separate directory...

Dockerfile → containers/Dockerfile

@@ -1,12 +1,10 @@
-# Test build with: docker buildx build --platform linux/amd64 -t colabfold_batch:1.5.2 --load .
-
 FROM condaforge/mambaforge
 
 ENV CONDA_PREFIX=/opt/conda
 ENV PATH /opt/conda/envs/colabfold_batch/bin:$PATH
 
-COPY colabfold_batch.yaml .
-COPY setup.sh .
+COPY ../colabfold_batch.yaml .
+COPY ../setup.sh .
 
 RUN ./setup.sh && \
 	rm colabfold_batch.yaml setup.sh && \

containers/build_image.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+# Builds a docker image with versioning extracted from yaml file
+# This uses 'buildx' for a cross-platform build allowing it be be built on MacOS 
+# where we have Docker available, then the image can be transferred to the cluster
+# and singuliarity used to create a .sif image. 
+
+# Doing a direct singularity build requires sudo access, or can be run on MacOS 
+# in a VM....
+
+version=$(grep "ColabFold.git" ../colabfold_batch.yaml|cut -d@ -f3|sed 's/^v//')
+echo "Building version ${version}..."
+
+docker buildx build --platform linux/amd64 -t colabfold_batch:${version} --load .
+docker save colabfold_batch:${version} > colabfold_batch.${version}.tar

containers/run_colabfold_singularity.sh

@@ -0,0 +1,13 @@
+#!/bin/env bash
+
+#$ -adds l_hard gpu 1
+#$ -adds l_hard cuda.0.name 'NVIDIA A40'
+#$ -j y
+#$ -N colabfold
+#$ -o colabfold_logs/$JOB_NAME.o$JOB_ID
+#$ -cwd
+
+
+
+singularity exec --nv -B .:/mnt /cluster/gjb_lab/jabbott/singularity/colabfold_batch.1.5.2.sif \
+	colabfold_batch /mnt/cadh5_arath.fa /mnt/colabfold_output