adding biocontainers example install script (#613)

* adding biocontainers example install script

Signed-off-by: vsoch <[email protected]>

Author: vsoch

example/README.md

@@ -0,0 +1,12 @@
+# Examples
+
+This set of examples includes the following:
+
+## Biocontainers Update
+
+The intention of this script is to instantiate a client, and then match
+containers you have in some root from [Galaxy Project Depot](https://depot.galaxyproject.org/singularity/)
+on your local filesytem to install to an shpc registry (as modules). The script
+tries to be efficient and instantiate one remote registry that has all the containers.
+
+### Usage

example/biocontainer-match.py

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+#!/usr/bin/env python3
+
+# Match biocontainers on the local filesystem to registry entries.
+# Install won't copy the container, but rather just use the provided path!
+# You should still set up your module_base before doing this (as we need
+# to write module files.
+
+# **ALWAYS** dry run first!
+#      python biocontainer-match.py --dry-run
+# At the root of your depot do:
+#      python biocontainer-match.py
+# Force module reinstall (rewrite of module file)
+#      python biocontainer-match.py --force
+# From another directory do:
+#     python biocontainer-match.py --containers /path/to/depot/root
+# If the namespace ever changes:
+#     python biocontainer-match.py --containers /path/to/depot/root --namespace quay.io/biocontainers
+# Only one namespace is currently supported!
+
+import argparse
+import os
+import re
+import sys
+
+from shpc.logger import logger
+from shpc.main import get_client
+
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        description="SHPC BioContainer Adder",
+        formatter_class=argparse.RawTextHelpFormatter,
+    )
+    parser.add_argument(
+        "--dry-run",
+        help="Dry run only! This will preview installs.",
+        default=False,
+        action="store_true",
+    )
+    parser.add_argument(
+        "--force", help="Force reinstall of module", default=False, action="store_true"
+    )
+    parser.add_argument("--containers", help="Path to depot root.", default=os.getcwd())
+    parser.add_argument(
+        "--namespace",
+        help="Namespace to use for containers (quay.io/biocontainers)",
+        default="quay.io/biocontainers",
+    )
+    return parser
+
+
+def main():
+
+    parser = get_parser()
+
+    # If an error occurs while parsing the arguments, the interpreter will exit with value 2
+    args, extra = parser.parse_known_args()
+
+    # Show args to the user
+    print(" containers: %s" % args.containers)
+
+    if not os.path.exists(args.containers):
+        sys.exit(f"Path {args.containers} does not exist.")
+    depot = os.path.abspath(args.containers)
+    cli = get_client()
+
+    # Keep a record of repos we've seen and don't repeat
+    seen = set()
+
+    # Ensure we start with the populated modules
+    cli.registry.iter_modules()
+
+    # Find all paths that match the pattern of a name:tag
+    for path in os.listdir(depot):
+        if not re.search("^(.*):(.*)$", path) or os.path.isdir(path):
+            continue
+        repo, tag = path.split(":", 1)
+
+        # Don't need to parse twice
+        if repo in seen:
+            continue
+
+        container = f"{args.namespace}/{repo}"
+        tagged = f"{container}:{tag}"
+
+        match = cli.registry.find(tagged)
+        if not match:
+            tagged = container
+            match = cli.registry.find(tagged)
+
+        if not match:
+            logger.warning(f"Warning: no match for {path}")
+            continue
+
+        if args.dry_run:
+            print(f"Would be installing {path} to {tagged}")
+            seen.add(repo)
+            continue
+
+        print(f"Installing {path} to {tagged}")
+
+        # We found a match! Install it (forcing keep path to not copy the container)
+        cli.install(tagged, force=args.force, container_image=path, keep_path=True)
+        seen.add(repo)
+
+
+if __name__ == "__main__":
+    main()