Allow data installs without Docker images present

Makes managing data from bcbio_vm.py easier. Thanks to discussion in bcbio/bcbio-nextgen#2473
bcbio · Nov 27, 2018 · 6c858cf · 6c858cf
1 parent 9fb1965
commit 6c858cf
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Showing 2 changed files with 19 additions and 6 deletions.
diff --git a/bcbiovm/docker/install.py b/bcbiovm/docker/install.py
@@ -36,8 +36,19 @@ def full(args, dockerconf):
             sys.exit(1)
         else:
             updates.append("biological data")
-        _check_docker_image(args)
-        manage.run_bcbio_cmd(args.image, dmounts, _get_cl(args))
+        if _check_docker_image(args, raise_error=False):
+            manage.run_bcbio_cmd(args.image, dmounts, _get_cl(args))
+        else:
+            args.upgrade = False
+            args.tools = False
+            args.tooldir = False
+            args.toolplus = False
+            args.isolate = True
+            args.distribution = None
+            args.cwl = True
+            print(args)
+            from bcbio import install
+            install.upgrade_bcbio(args)
     _save_install_defaults(args)
     if updates:
         print("\nbcbio-nextgen-vm updated with latest %s" % " and ".join(updates))
@@ -66,7 +77,7 @@ def upgrade_bcbio_vm():
     else:
         subprocess.check_call([conda_bin, "install", "-y", "-c", "conda-forge", "-c", "bioconda",
                                "bcbio-nextgen-vm", "bcbio-nextgen", "cwltool", "arvados-cwl-runner",
-                               "toil", "rabix-bunny"])
+                               "toil", "cromwell"])
 
 def pull(args, dockerconf):
     """Pull down latest docker image.
@@ -126,14 +137,15 @@ def add_install_defaults(args):
     args = _add_docker_defaults(args, default_args)
     return args
 
-def _check_docker_image(args):
+def _check_docker_image(args, raise_error=True):
     """Ensure docker image exists.
     """
     for image in subprocess.check_output(["docker", "images"]).split("\n"):
         parts = image.split()
         if len(parts) > 1 and parts[0] == args.image:
-            return
-    raise ValueError("Could not find docker image %s in local repository" % args.image)
+            return True
+    if raise_error:
+        raise ValueError("Could not find docker image %s in local repository" % args.image)
 
 def docker_image_arg(args):
     if not hasattr(args, "image") or not args.image:

diff --git a/scripts/bcbio_vm.py b/scripts/bcbio_vm.py
@@ -124,6 +124,7 @@ def _install_cmd(subparsers, name):
                           action="store_true", default=False)
     parser_i.add_argument("--image", help="Docker image name to use, could point to compatible pre-installed image.",
                           default=None)
+    parser_i.add_argument("--cores", help="Cores to use for parallel data prep processes", default=1, type=int)
     parser_i.set_defaults(func=cmd_install)
 
 def _std_config_args(parser):