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Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc

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mvdbeek
2024-06-21 16:58:21 +02:00
parent f5610e7780
commit 7c6fc1800f
15 changed files with 28 additions and 28 deletions
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config/job_conf.yml.interactivetools
+2 -2
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@@ -41,8 +41,8 @@ execution:
#docker_cmd: /usr/local/custom_docker/docker
#docker_host:
#docker_container_id_override: busybox:ubuntu-14.04
#docker_default_container_id: busybox:ubuntu-14.04
#docker_container_id_override: busybox:1.36.1-glibc
#docker_default_container_id: busybox:1.36.1-glibc
#require_container: true
#container_monitor: true
#container_monitor_result: file
doc/source/admin/jobs.md
+1 -1
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@@ -159,7 +159,7 @@ execution:
k8s_namespace: default
runner: pulsar_k8s
docker_enabled: true
docker_default_container_id: busybox:ubuntu-14.04
docker_default_container_id: busybox:1.36.1-glibc
pulsar_app_config:
message_queue_url: 'amqp://guest:guest@host.docker.internal:5672//'
local_environment:
doc/source/admin/special_topics/interactivetools.rst
+2 -2
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@@ -172,8 +172,8 @@ An example ``job_conf.yml`` file as seen in ``config/job_conf.yml.interactivetoo
#docker_cmd: /usr/local/custom_docker/docker
#docker_host:
#docker_container_id_override: busybox:ubuntu-14.04
#docker_default_container_id: busybox:ubuntu-14.04
#docker_container_id_override: busybox:1.36.1-glibc
#docker_default_container_id: busybox:1.36.1-glibc
#require_container: true
#container_monitor: true
#container_monitor_result: file
doc/source/admin/special_topics/mulled_containers.rst
+1 -1
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@@ -16,7 +16,7 @@ requirement field.
<requirements>
<!-- Container based dependency handling -->
<container type="docker">busybox:ubuntu-14.04</container>
<container type="docker">busybox:1.36.1-glibc</container>
<!-- Conda based dependency handling -->
<requirement type="package" version="8.22">gnu_coreutils</requirement>
</requirements>
lib/galaxy/config/sample/job_conf.sample.yml
+4 -4
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@@ -513,13 +513,13 @@ execution:
# trust tool's specified container - a destination wide override
# can be set. This will cause all jobs on this destination to use
# that docker image.
#docker_container_id_override: busybox:ubuntu-14.04
#docker_container_id_override: busybox:1.36.1-glibc
# Likewise, if deployer wants to use docker for isolation and
# does trust tool's specified container - but also wants tool's not
# configured to run in a container the following option can provide
# a fallback. -->
#docker_default_container_id: busybox:ubuntu-14.04
#docker_default_container_id: busybox:1.36.1-glibc
# If the destination should be secured to only allow containerized jobs
# the following parameter may be set for the job destination. Some tools
@@ -633,7 +633,7 @@ execution:
- type: docker
shell: '/bin/sh'
resolve_dependencies: false
identifier: 'busybox:ubuntu-14.04'
identifier: 'busybox:1.36.1-glibc'
- type: singularity
shell: '/bin/sh'
resolve_dependencies: false
@@ -642,7 +642,7 @@ execution:
- type: docker
shell: '/bin/sh'
resolve_dependencies: false
identifier: 'busybox:ubuntu-14.04'
identifier: 'busybox:1.36.1-glibc'
- type: singularity
shell: '/bin/sh'
resolve_dependencies: false
lib/galaxy/config/sample/job_conf.xml.sample_advanced
+5 -5
View File
@@ -588,13 +588,13 @@
trust tool's specified container - a destination wide override
can be set. This will cause all jobs on this destination to use
that docker image. -->
<!-- <param id="docker_container_id_override">busybox:ubuntu-14.04</param> -->
<!-- <param id="docker_container_id_override">busybox:1.36.1-glibc'</param> -->
<!-- Likewise, if deployer wants to use docker for isolation and
does trust tool's specified container - but also wants tool's not
configured to run in a container the following option can provide
a fallback. -->
<!-- <param id="docker_default_container_id">busybox:ubuntu-14.04</param> -->
<!-- <param id="docker_default_container_id">busybox:1.36.1-glibc'</param> -->
<!-- If the destination should be secured to only allow containerized jobs
the following parameter may be set for the job destination. Some tools do
@@ -674,11 +674,11 @@
the enabled container types for this destination will be used.
-->
<param id="container_override">
<container type="docker" shell="/bin/sh" resolve_dependencies="false">busybox:ubuntu-14.04</container>
<container type="docker" shell="/bin/sh" resolve_dependencies="false">busybox:1.36.1-glibc'</container>
<container type="singularity" shell="/bin/sh" resolve_dependencies="false">/path/to/default/container</container>
</param>
<param id="container">
<container type="docker" shell="/bin/sh" resolve_dependencies="false">busybox:ubuntu-14.04</container>
<container type="docker" shell="/bin/sh" resolve_dependencies="false">busybox:1.36.1-glibc'</container>
<container type="singularity" shell="/bin/sh" resolve_dependencies="false">/path/to/default/container</container>
</param>
</destination>
@@ -966,7 +966,7 @@
container ID will be passed along to condor as
the docker_image submission parameter.
-->
<!-- <param id="docker_default_container_id">busybox:ubuntu-14.04</param> -->
<!-- <param id="docker_default_container_id">busybox:1.36.1-glibc'</param> -->
</destination>
<!-- Jobs can be re-submitted for various reasons (to the same destination or others,
test/functional/tools/catDocker.xml
+1 -1
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@@ -1,7 +1,7 @@
<tool id="catdc" name="Concatenate datasets (in docker)" version="1.0.0">
<description>tail-to-head</description>
<requirements>
<container type="docker">busybox:ubuntu-14.04</container>
<container type="docker">busybox:1.36.1-glibc</container>
</requirements>
<command><![CDATA[
echo "Galaxy slots passed through contain as \$GALAXY_SLOTS" &&
test/functional/tools/job_environment_default.xml
+1 -1
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@@ -1,6 +1,6 @@
<tool id="job_environment_default" name="job_environment_default" version="0.1.0" profile="18.01">
<requirements>
<container type="docker">busybox:ubuntu-14.04</container>
<container type="docker">busybox:1.36.1-glibc</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[
mktemp -d &&
test/functional/tools/job_environment_default_legacy.xml
+1 -1
View File
@@ -1,6 +1,6 @@
<tool id="job_environment_default_legacy" name="job_environment_default_legacy" version="0.1.0">
<requirements>
<container type="docker">busybox:ubuntu-14.04</container>
<container type="docker">busybox:1.36.1-glibc</container>
</requirements>
<command detect_errors="exit_code"><![CDATA[
mktemp -d &&
test/functional/tools/job_environment_explicit_isolated_home.xml
+1 -1
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@@ -1,6 +1,6 @@
<tool id="job_environment_explicit_isolated_home" name="job_environment_explicit_isolated_home" version="0.1.0">
<requirements>
<container type="docker">busybox:ubuntu-14.04</container>
<container type="docker">busybox:1.36.1-glibc</container>
</requirements>
<command use_shared_home="false"><![CDATA[
mktemp -d &&
test/functional/tools/job_environment_explicit_shared_home.xml
+1 -1
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@@ -1,6 +1,6 @@
<tool id="job_environment_explicit_shared_home" name="job_environment_explicit_shared_home" version="0.1.0" profile="18.01">
<requirements>
<container type="docker">busybox:ubuntu-14.04</container>
<container type="docker">busybox:1.36.1-glibc</container>
</requirements>
<command use_shared_home="true"><![CDATA[
mktemp -d &&
test/functional/tools/tool_directory_docker.xml
+1 -1
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@@ -1,6 +1,6 @@
<tool id="tool_directory_docker" name="tool_directory_docker" version="1.0.0">
<requirements>
<container type="docker">busybox:ubuntu-14.04</container>
<container type="docker">busybox:1.36.1-glibc</container>
</requirements>
<command><![CDATA[
cp '$__tool_directory__/tool_directory.xml' output1
test/integration/test_coexecution.py
+3 -3
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@@ -66,7 +66,7 @@ execution:
k8s_namespace: ${k8s_namespace}
runner: pulsar_k8s
docker_enabled: true
docker_default_container_id: busybox:ubuntu-14.04
docker_default_container_id: busybox:1.36.1-glibc
pulsar_app_config:
message_queue_url: '${container_amqp_url}'
env:
@@ -145,7 +145,7 @@ execution:
runner: pulsar_tes
tes_url: ${tes_url}
docker_enabled: true
docker_default_container_id: busybox:ubuntu-14.04
docker_default_container_id: busybox:1.36.1-glibc
pulsar_app_config:
message_queue_url: '${container_amqp_url}'
env:
@@ -204,7 +204,7 @@ execution:
runner: pulsar_tes
tes_url: ${tes_url}
docker_enabled: true
docker_default_container_id: busybox:ubuntu-14.04
docker_default_container_id: busybox:1.36.1-glibc
pulsar_app_config:
message_queue_url: '${container_amqp_url}'
env:
test/integration/test_kubernetes_runner.py
+3 -3
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@@ -133,21 +133,21 @@ def job_config(jobs_directory: str) -> Config:
<param id="limits_cpu">1.1</param>
<param id="limits_memory">100M</param>
<param id="docker_enabled">true</param>
<param id="docker_default_container_id">busybox:ubuntu-14.04</param>
<param id="docker_default_container_id">busybox:1.36.1-glibc</param>
<env id="SOME_ENV_VAR">42</env>
</destination>
<destination id="k8s_destination_walltime_short" runner="k8s_walltime_short">
<param id="limits_cpu">1.1</param>
<param id="limits_memory">100M</param>
<param id="docker_enabled">true</param>
<param id="docker_default_container_id">busybox:ubuntu-14.04</param>
<param id="docker_default_container_id">busybox:1.36.1-glibc</param>
<env id="SOME_ENV_VAR">42</env>
</destination>
<destination id="k8s_destination_no_cleanup" runner="k8s_no_cleanup">
<param id="limits_cpu">1.1</param>
<param id="limits_memory">100M</param>
<param id="docker_enabled">true</param>
<param id="docker_default_container_id">busybox:ubuntu-14.04</param>
<param id="docker_default_container_id">busybox:1.36.1-glibc</param>
<env id="SOME_ENV_VAR">42</env>
</destination>
<destination id="local_dest" runner="local">
test/unit/app/jobs/test_job_configuration.py
+1 -1
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@@ -322,7 +322,7 @@ class TestAdvancedJobConfXmlParser(BaseJobConfXmlParserTestCase):
assert len(container) == 2
container0 = container[0]
assert container0["type"] == "docker"
assert container0["identifier"] == "busybox:ubuntu-14.04"
assert container0["identifier"] == "busybox:1.36.1-glibc"
container_override = container_dest.params["container_override"]
assert len(container_override) == 2