Merge pull request #84 from galaxyproject/tripple

make multitool-container generation a little bit more stable

galaxy/tools/deps/mulled/invfile.lua

@@ -42,7 +42,7 @@ end
 
 local conda_image = VAR.CONDA_IMAGE
 if conda_image == '' then
-    conda_image = 'continuumio/miniconda:latest'
+    conda_image = 'continuumio/miniconda3:latest'
 end
 
 
@@ -104,8 +104,8 @@ if VAR.SINGULARITY ~= '' then
         .withHostConfig({binds = {"build:/data",singularity_image_dir .. ":/import"}, privileged = true})
         .withConfig({entrypoint = {'/bin/sh', '-c'}})
         -- for small containers (less than 7MB), double the size otherwise, add a little bit more as half the conda size
-        .run("size=$(du -sc  /data/dist/ | tail -n 1 | cut -f 1 | awk '{print int($1/1024)}' ) && if [ $size -lt '7' ]; then echo $(($size*2)); else  echo $(($size+$size*7/10)); fi")
-        .run("singularity create --size `size=$(du -sc /data/dist/ | tail -n 1 | cut -f 1 | awk '{print int($1/1024)}' ) && if [ $size -lt '7' ]; then echo $(($size*2)); else  echo $(($size+$size*7/10)); fi` /import/" .. VAR.SINGULARITY_IMAGE_NAME)
+        .run("size=$(du -sc  /data/dist/ | tail -n 1 | cut -f 1 | awk '{print int($1/1024)}' ) && if [ $size -lt '10' ]; then echo 20; else  echo $(($size+$size*7/10)); fi")
+        .run("singularity create --size `size=$(du -sc /data/dist/ | tail -n 1 | cut -f 1 | awk '{print int($1/1024)}' ) && if [ $size -lt '10' ]; then echo 20; else  echo $(($size+$size*7/10)); fi` /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

galaxy/tools/deps/mulled/mulled_build.py

@@ -33,14 +33,15 @@
     conda_build_target_str,
     create_repository,
     quay_repository,
+    PrintProgress,
     v1_image_name,
     v2_image_name,
 )
 from ..conda_compat import MetaData
 
 DIRNAME = os.path.dirname(__file__)
 DEFAULT_CHANNEL = "bioconda"
-DEFAULT_EXTRA_CHANNELS = ["conda-forge", "r"]
+DEFAULT_EXTRA_CHANNELS = ["conda-forge"]
 DEFAULT_CHANNELS = [DEFAULT_CHANNEL] + DEFAULT_EXTRA_CHANNELS
 DEFAULT_REPOSITORY_TEMPLATE = "quay.io/${namespace}/${image}"
 DEFAULT_BINDS = ["build/dist:/usr/local/"]
@@ -242,7 +243,8 @@ def mull_targets(
             with open(os.path.join(singularity_image_dir, 'Singularity'), 'w+') as sin_def:
                 fill_template = SINGULARITY_TEMPLATE % {'container_test': test}
                 sin_def.write(fill_template)
-        ret = involucro_context.exec_command(involucro_args)
+        with PrintProgress():
+            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

galaxy/tools/deps/mulled/mulled_build_files.py

@@ -15,6 +15,7 @@
 import collections
 import glob
 import os
+import sys
 
 from ._cli import arg_parser
 from .mulled_build import (
@@ -36,14 +37,17 @@ def main(argv=None):
     args = parser.parse_args()
     for (targets, image_build, name_override) in generate_targets(args.files):
         try:
-            mull_targets(
+            ret = mull_targets(
                 targets,
                 image_build=image_build,
                 name_override=name_override,
                 **args_to_mull_targets_kwds(args)
             )
         except BuildExistsException:
             continue
+        if ret > 0:
+            sys.exit(ret)
+
 
 
 def generate_targets(target_source):

galaxy/tools/deps/mulled/util.py

@@ -3,6 +3,9 @@
 
 import collections
 import hashlib
+import time
+import threading
+import sys
 
 from distutils.version import LooseVersion
 
@@ -207,6 +210,27 @@ def v2_image_name(targets, image_build=None, name_override=None):
         return "mulled-v2-%s%s" % (package_hash.hexdigest(), suffix)
 
 
+class PrintProgress:
+    def __init__(self):
+        self.thread = threading.Thread(target=self.progress)
+        self.stop = False
+
+    def progress(self):
+        while not self.stop:
+            print(".", end="")
+            sys.stdout.flush()
+            time.sleep(60)
+        print("")
+
+    def __enter__(self):
+        self.thread.start()
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        self.stop = True
+        self.thread.join()
+
+
 image_name = v1_image_name  # deprecated
 
 __all__ = (