From 05fbef510c7497911a2abea83c5bdc26bf338460 Mon Sep 17 00:00:00 2001 From: Anthony Bretaudeau Date: Fri, 28 Oct 2016 12:02:30 +0200 Subject: [PATCH 1/4] Add doc for conda_copy_dependencies option Discussed on IUC gitter, related to https://github.com/galaxyproject/galaxy/issues/3008 --- config/galaxy.ini.sample | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index 9d5dc4050a9..042923c54fc 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -212,6 +212,11 @@ paste.app_factory = galaxy.web.buildapp:app_factory # 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 +# Set to True if conda_prefix and job_working_directory are not on the same +# volume. Conda will copy packages content instead of creating symlinks. +# This will prevent problems with some specific packages (perl, R), at the cost +# of extra disk space usage. +#conda_copy_dependencies = False # 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). From 16866b5e8075d648bd17ac3786f76356e23c43a2 Mon Sep 17 00:00:00 2001 From: Anthony Bretaudeau Date: Fri, 28 Oct 2016 12:13:33 +0200 Subject: [PATCH 2/4] add extra time problem --- config/galaxy.ini.sample | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index 042923c54fc..55b2bdfc19b 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -215,7 +215,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory # Set to True if conda_prefix and job_working_directory are not on the same # volume. Conda will copy packages content instead of creating symlinks. # This will prevent problems with some specific packages (perl, R), at the cost -# of extra disk space usage. +# of extra disk space usage and extra time spent copying packages. #conda_copy_dependencies = False # File containing the Galaxy Tool Sheds that should be made available to From 69cda7ee10d78a61830f90f957500ba41821640b Mon Sep 17 00:00:00 2001 From: Anthony Bretaudeau Date: Fri, 28 Oct 2016 12:21:32 +0200 Subject: [PATCH 3/4] clarify links --- config/galaxy.ini.sample | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index 55b2bdfc19b..a7e870bb88f 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -212,8 +212,8 @@ paste.app_factory = galaxy.web.buildapp:app_factory # 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 -# Set to True if conda_prefix and job_working_directory are not on the same -# volume. Conda will copy packages content instead of creating symlinks. +# You can set this to True if conda_prefix and job_working_directory are not on the same +# volume. Conda will copy packages content instead of creating hardlinks or symlinks. # This will prevent problems with some specific packages (perl, R), at the cost # of extra disk space usage and extra time spent copying packages. #conda_copy_dependencies = False From 8a972cc325fd39b71d89f28d9eec62630d9859ac Mon Sep 17 00:00:00 2001 From: Anthony Bretaudeau Date: Mon, 7 Nov 2016 11:03:41 +0100 Subject: [PATCH 4/4] be stronger --- config/galaxy.ini.sample | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index a7e870bb88f..fed62f94e34 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -212,8 +212,9 @@ paste.app_factory = galaxy.web.buildapp:app_factory # 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 -# You can set this to True if conda_prefix and job_working_directory are not on the same -# volume. Conda will copy packages content instead of creating hardlinks or symlinks. +# You must set this to True if conda_prefix and job_working_directory are not on the same +# volume, or some conda dependencies will fail to execute at job runtime. +# Conda will copy packages content instead of creating hardlinks or symlinks. # This will prevent problems with some specific packages (perl, R), at the cost # of extra disk space usage and extra time spent copying packages. #conda_copy_dependencies = False