<commit_before># Galaxy - Irida Integration Testing Image
#
#

FROM apetkau/snvphyl-galaxy-0.3

MAINTAINER <NAME>, <EMAIL>

ENV GALAXY_CONFIG_BRAND Irida Integration Testing

WORKDIR /galaxy-central

ENV GALAXY_TEST_TOOL_CONF /galaxy-central/config/tool_conf.xml.sample

# Add test tool and tool shed configs
ADD ./galaxy/tool_conf_irida.xml /galaxy-central/config/tool_conf.xml.sample
ADD ./galaxy/tool_sheds_conf.xml /etc/galaxy/tool_sheds_conf.xml
#ADD ./galaxy/universe.sqlite /galaxy-central/database/universe.sqlite
# add prepopulated database to the container

RUN sed -i -e 's/#admin_users = None/admin_users = <EMAIL>,<EMAIL>/' /etc/galaxy/galaxy.ini
#RUN sed -i -e 's$#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE$database_connection = mysql://test:test@localhost/irida_galaxy_test?unix_socket=/var/run/mysqld/mysqld.sock$' /etc/galaxy/galaxy.ini
#RUN sed -i -e 's$#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE$database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE$' /etc/galaxy/galaxy.ini

# Add custom Irida tools to Galaxy
ADD ./galaxy/assembly_annotation_pipeline_outputs.xml /galaxy-central/tools/irida/assembly_annotation_pipeline_outputs.xml
ADD ./galaxy/collection_list_paired.xml /galaxy-central/tools/irida/collection_list_paired.xml
ADD ./galaxy/core_pipeline_outputs.xml /galaxy-central/tools/irida/core_pipeline_outputs.xml
ADD ./galaxy/core_pipeline_outputs_paired.xml /galaxy-central/tools/irida/core_pipeline_outputs_paired.xml
ADD ./galaxy/core_pipeline_outputs_paired_with_multi_level_parameters.xml /galaxy-central/tools/irida/core_pipeline_outputs_paired_with_multi_level_parameters.xml<commit_msg>Disable `force_beta_workflow_scheduled_for_collections` to fix SNVPhyl tests with docker-galaxy.<commit_after># Galaxy - Irida Integration Testing Image
#
#

FROM apetkau/snvphyl-galaxy-0.3

MAINTAINER <NAME>, <EMAIL>

ENV GALAXY_CONFIG_BRAND Irida Integration Testing

WORKDIR /galaxy-central

ENV GALAXY_TEST_TOOL_CONF /galaxy-central/config/tool_conf.xml.sample

# Add test tool and tool shed configs
ADD ./galaxy/tool_conf_irida.xml /galaxy-central/config/tool_conf.xml.sample
ADD ./galaxy/tool_sheds_conf.xml /etc/galaxy/tool_sheds_conf.xml

RUN sed -i -e 's/#admin_users = None/admin_users = <EMAIL>,workflow<EMAIL>/' /etc/galaxy/galaxy.ini
RUN sed -i -e 's/force_beta_workflow_scheduled_for_collections=False/force_beta_workflow_scheduled_for_collections=True/' /etc/galaxy/galaxy/ini

# Add custom Irida tools to Galaxy
ADD ./galaxy/assembly_annotation_pipeline_outputs.xml /galaxy-central/tools/irida/assembly_annotation_pipeline_outputs.xml
ADD ./galaxy/collection_list_paired.xml /galaxy-central/tools/irida/collection_list_paired.xml
ADD ./galaxy/core_pipeline_outputs.xml /galaxy-central/tools/irida/core_pipeline_outputs.xml
ADD ./galaxy/core_pipeline_outputs_paired.xml /galaxy-central/tools/irida/core_pipeline_outputs_paired.xml
ADD ./galaxy/core_pipeline_outputs_paired_with_multi_level_parameters.xml /galaxy-central/tools/irida/core_pipeline_outputs_paired_with_multi_level_parameters.xml
{'fraction_non_alphanumeric': 0.10390848427073403, 'fraction_numerical': 0.001271051795360661, 'mean_word_length': 6.170842824601367, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 11, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 30}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3694680', 'n_tokens_mistral': 1142, 'n_tokens_neox': 1110, 'n_words': 163}