Merged downstream galaxy-lib mulled enhancement and fixes.

- Singularity support for building mulled containers https://github.com/galaxyproject/galaxy-lib/pull/64
- Hack to fix previous mulled v2 changes for single requirement tools https://github.com/galaxyproject/galaxy-lib/pull/65.

lib/galaxy/tools/deps/mulled/invfile.lua

@@ -45,6 +45,13 @@ if conda_image == '' then
     conda_image = 'continuumio/miniconda:latest'
 end
 
+
+local singularity_image = VAR.SINGULARITY_IMAGE
+if singularity_image == '' then
+    singularity_image = 'quay.io/biocontainers/singularity:2.3--0'
+end
+
+
 local destination_base_image = VAR.DEST_BASE_IMAGE
 if destination_base_image == '' then
     destination_base_image = 'bgruening/busybox-bash:0.1'
@@ -84,9 +91,25 @@ inv.task('build')
         .at('/usr/local')
         .inImage(destination_base_image)
         .as(repo)
+
+if VAR.SINGULARITY ~= '' then
+    inv.task('singularity')
+        .using(singularity_image)
+        .withHostConfig({binds = {"build:/data","singularity_import:/import"}, privileged = true})
+        .withConfig({entrypoint = {'/bin/sh', '-c'}})
+        -- this will create a container that is the size of our conda dependencies + 20MiB
+        -- The 20 MiB can be improved at some point, but this seems to work for now.
+        .run("du -sc  /data/dist/ | tail -n 1 | cut -f 1 | awk '{print int($1/1024)+20}'")
+        .run("singularity create --size `du -sc  /data/dist/ | tail -n 1 | cut -f 1 | awk '{print int($1/1024)+20}'` /import/" .. VAR.SINGULARITY_IMAGE_NAME)
+        .run('mkdir -p /usr/local/var/singularity/mnt/container && singularity bootstrap /import/' .. VAR.SINGULARITY_IMAGE_NAME .. ' /import/Singularity')
+        .run('chown ' .. VAR.USER_ID .. ' /import/' .. VAR.SINGULARITY_IMAGE_NAME)
+end
+
+inv.task('cleanup')
     .using(conda_image)
-        .withHostConfig({binds = {"build:/data"}})
-        .run('rm', '-rf', '/data/dist')
+    .withHostConfig({binds = {"build:/data"}})
+    .run('rm', '-rf', '/data/dist')
+
 
 if VAR.TEST_BINDS == '' then
     inv.task('test')
@@ -106,9 +129,14 @@ inv.task('push')
 
 inv.task('build-and-test')
     .runTask('build')
+    .runTask('singularity')
+    .runTask('cleanup')
     .runTask('test')
 
+
 inv.task('all')
     .runTask('build')
+    .runTask('singularity')
+    .runTask('cleanup')
     .runTask('test')
     .runTask('push')

lib/galaxy/tools/deps/mulled/mulled_build.py

@@ -47,6 +47,23 @@ IS_OS_X = _platform == "darwin"
 INVOLUCRO_VERSION = "1.1.2"
 DEST_BASE_IMAGE = os.environ.get('DEST_BASE_IMAGE', None)
 
+SINGULARITY_TEMPLATE = """Bootstrap: docker
+From: bgruening/busybox-bash:0.1
+
+%%setup
+
+    echo "Copying conda environment"
+    mkdir -p /tmp/conda
+    cp -r /data/dist/* /tmp/conda/
+
+%%post
+    mkdir -p /usr/local
+    cp -R /tmp/conda/* /usr/local/
+
+%%test
+    %(container_test)s
+"""
+
 
 def involucro_link():
     if IS_OS_X:
@@ -134,17 +151,21 @@ def mull_targets(
     test='true', test_files=None, image_build=None, name_override=None,
     repository_template=DEFAULT_REPOSITORY_TEMPLATE, dry_run=False,
     conda_version=None, verbose=False, binds=DEFAULT_BINDS, rebuild=True,
-    oauth_token=None, hash_func="v2",
+    oauth_token=None, hash_func="v2", singularity=False,
 ):
     targets = list(targets)
     if involucro_context is None:
         involucro_context = InvolucroContext()
 
     image_function = v1_image_name if hash_func == "v1" else v2_image_name
+    if len(targets) > 2 and image_build is None:
+        # Force an image build in this case - this seems hacky probably
+        # shouldn't work this way but single case broken else wise.
+        image_build = "0"
 
     repo_template_kwds = {
         "namespace": namespace,
-        "image": image_function(targets, image_build=image_build or '0', name_override=name_override)
+        "image": image_function(targets, image_build=image_build, name_override=name_override)
     }
     repo = string.Template(repository_template).safe_substitute(repo_template_kwds)
 
@@ -187,6 +208,11 @@ def mull_targets(
         involucro_args.extend(["-set", "DEST_BASE_IMAGE='%s'" % DEST_BASE_IMAGE])
     if verbose:
         involucro_args.extend(["-set", "VERBOSE='1'"])
+    if singularity:
+        singularity_image_name = repo_template_kwds['image']
+        involucro_args.extend(["-set", "SINGULARITY='1'"])
+        involucro_args.extend(["-set", "SINGULARITY_IMAGE_NAME='%s'" % singularity_image_name])
+        involucro_args.extend(["-set", "USER_ID='%s:%s'" % (os.getuid(), os.getgid() )])
     if conda_version is not None:
         verbose = "--verbose" if verbose else "--quiet"
         involucro_args.extend(["-set", "PREINSTALL='conda install %s --yes conda=%s'" % (verbose, conda_version)])
@@ -206,7 +232,18 @@ def mull_targets(
     print(" ".join(involucro_context.build_command(involucro_args)))
     if not dry_run:
         ensure_installed(involucro_context, True)
-        return involucro_context.exec_command(involucro_args)
+        if singularity:
+            if not os.path.exists('./singularity_import'):
+                os.mkdir('./singularity_import')
+            with open('./singularity_import/Singularity', 'w+') as sin_def:
+                fill_template = SINGULARITY_TEMPLATE % {'container_test': test}
+                sin_def.write(fill_template)
+        ret = involucro_context.exec_command(involucro_args)
+        if singularity:
+            # we can not remove this folder as it contains the image wich is owned by root
+            pass
+            # shutil.rmtree('./singularity_import')
+        return ret
     return 0
 
 
@@ -275,6 +312,8 @@ def add_build_arguments(parser):
                         help='Just print commands instead of executing them.')
     parser.add_argument('--verbose', dest='verbose', action="store_true",
                         help='Cause process to be verbose.')
+    parser.add_argument('--singularity', action="store_true",
+                        help='Additionally build a singularity image.')
     parser.add_argument('-n', '--namespace', dest='namespace', default="biocontainers",
                         help='quay.io namespace.')
     parser.add_argument('-r', '--repository_template', dest='repository_template', default=DEFAULT_REPOSITORY_TEMPLATE,
@@ -324,6 +363,8 @@ def args_to_mull_targets_kwds(args):
         kwds["namespace"] = args.namespace
     if hasattr(args, "dry_run"):
         kwds["dry_run"] = args.dry_run
+    if hasattr(args, "singularity"):
+        kwds["singularity"] = args.singularity
     if hasattr(args, "test"):
         kwds["test"] = args.test
     if hasattr(args, "test_files"):