From 9d467ddd5204deafb3a0dadae7813691e24c7c3c Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Tue, 9 Aug 2016 13:34:18 -0400 Subject: [PATCH 1/3] enable conda_auto_init in sample, adjust wording --- config/galaxy.ini.sample | 28 +++++++++++++++------------- lib/galaxy/tools/deps/__init__.py | 2 +- 2 files changed, 16 insertions(+), 14 deletions(-) diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index b00e3faf0de..b6e81983c9e 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -164,29 +164,31 @@ paste.app_factory = galaxy.web.buildapp:app_factory # tag. #tool_path = tools +# -- Tool dependencies + # Path to the directory in which tool dependencies are placed. This is used by -# the tool shed to install dependencies and can also be used by administrators +# the Tool Shed to install dependencies and can also be used by administrators # to manually install or link to dependencies. For details, see: # https://wiki.galaxyproject.org/Admin/Config/ToolDependencies # Set to the string none to explicitly disable tool dependency handling. # If this option is set to none or an invalid path, installing tools with dependencies -# from the Tool Shed will fail. +# from the Tool Shed will fail. #tool_dependency_dir = database/dependencies -# The dependency resolves config file specifies an ordering and options for how +# The dependency resolvers config file specifies an ordering and options for how # Galaxy resolves tool dependencies (requirement tags in Tool XML). The default -# ordering is to the use the tool shed for tools installed that way, use local -# Galaxy packages, and then use conda if available. +# ordering is to the use the Tool Shed for tools installed that way, use local +# Galaxy packages, and then use Conda if available. # See https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/dependency_resolvers.rst # for more information on these options. #dependency_resolvers_config_file = config/dependency_resolvers_conf.xml -# Following conda dependeny resolution options are experimental as of early -# 2016. These will change the defaults for each conda resolver, but multiple -# resolvers can be configured independently and these options overridden in +# Following Conda dependency resolution options will change the defaults for each Conda resolver, +# but multiple resolvers can be configured independently and these options overridden in # dependency_resolvers_config_file. +# Location on the filesystem where Conda packages are installed #conda_prefix = /_conda -# Override the conda executable to use, it will default to the one on the +# Override the Conda executable to use, it will default to the one on the # PATH (if available) and then to /bin/conda #conda_exec = # Pass debug flag to conda commands. @@ -196,11 +198,11 @@ paste.app_factory = galaxy.web.buildapp:app_factory # Set to True to instruct Galaxy to look for and install missing tool # dependencies before each job runs. #conda_auto_install = False -# Set to True to perform additional checking of installed conda environment +# Set to True to perform additional checking of installed Conda environment #conda_verbose_install_check=False -# Set to True to instruct Galaxy to install conda from the web automatically +# Set to True to instruct Galaxy to install Conda from the web automatically # if it cannot find a local copy and conda_exec is not configured. -#conda_auto_init = False +#conda_auto_init = True # File containing the Galaxy Tool Sheds that should be made available to # install from in the admin interface (.sample used if default does not exist). @@ -1212,7 +1214,7 @@ use_interactive = True #communication_server_host = http://localhost #communication_server_port = 7070 # persistent_communication_rooms is a comma-separated list of rooms that should be always available. -#persistent_communication_rooms = +#persistent_communication_rooms = # ---- Galaxy External Message Queue ------------------------------------------------- diff --git a/lib/galaxy/tools/deps/__init__.py b/lib/galaxy/tools/deps/__init__.py index f7afa8e8a65..65971dfc825 100644 --- a/lib/galaxy/tools/deps/__init__.py +++ b/lib/galaxy/tools/deps/__init__.py @@ -22,7 +22,7 @@ EXTRA_CONFIG_KWDS = { 'conda_debug': None, 'conda_ensure_channels': 'r,bioconda,iuc', 'conda_auto_install': False, - 'conda_auto_init': False, + 'conda_auto_init': True, } CONFIG_VAL_NOT_FOUND = object() From fd3c8753706491e1f6c261d58f42842bfe2757ec Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Tue, 9 Aug 2016 23:16:58 +0200 Subject: [PATCH 2/3] Fix string substitution --- lib/galaxy/tools/deps/resolvers/conda.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py index 449bca910f6..0e1e5983a29 100644 --- a/lib/galaxy/tools/deps/resolvers/conda.py +++ b/lib/galaxy/tools/deps/resolvers/conda.py @@ -53,7 +53,7 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In # warning is related to conda problem discussed in https://github.com/galaxyproject/galaxy/issues/2537, remove when that is resolved conda_prefix_warning_length = 50 if len(conda_prefix) >= conda_prefix_warning_length: - log.warning('Conda install prefix ({}) is long ({} characters), this can cause problems with package installation, consider setting a shorter prefix (conda_prefix in galaxy.ini)') + log.warning("Conda install prefix '%s' is %d characters long, this can cause problems with package installation, consider setting a shorter prefix (conda_prefix in galaxy.ini)" % (conda_prefix, len(conda_prefix))) condarc_override = get_option("condarc_override") if condarc_override is None: From e35c6295694c4065fc880e00fabe43f0c1905748 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Wed, 10 Aug 2016 19:23:17 +0200 Subject: [PATCH 3/3] Extend startup time --- .ci/first_startup.sh | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/.ci/first_startup.sh b/.ci/first_startup.sh index 8b7453bef12..e0700d9e81e 100644 --- a/.ci/first_startup.sh +++ b/.ci/first_startup.sh @@ -1,6 +1,15 @@ +#!/bin/bash +TRIES=120 +URL=http://localhost:8080 echo "Testing for correct startup:" -bash run.sh --daemon && sleep 30s && curl -I localhost:8080 -EXIT_CODE=$? +bash run.sh --daemon && \ +while [[ $i -le $TRIES ]] +do + curl "$URL" && EXIT_CODE=0 && break + sleep 1 + EXIT_CODE=1 + ((i = i + 1)) +done echo "exit code:$EXIT_CODE, showing startup log:" cat paster.log exit $EXIT_CODE