From 80febae523c133b296bf88d07d0022adc1146a43 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Sun, 7 Jul 2019 17:20:24 +0200 Subject: [PATCH 1/2] Pass through tool defined environment_variables to Docker. --- lib/galaxy/tools/__init__.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index 7beabc880b3..e9490bb99d0 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -705,6 +705,10 @@ class Tool(Dictifiable): self.home_target = home_target self.tmp_target = tmp_target self.docker_env_pass_through = tool_source.parse_docker_env_pass_through() + if self.environment_variables: + if not self.docker_env_pass_through: + self.docker_env_pass_through = [] + self.docker_env_pass_through.extend(map(lambda x: x['name'], self.environment_variables)) # Parameters used to build URL for redirection to external app redirect_url_params = tool_source.parse_redirect_url_params_elem() From a91420096568e54c2529ea04b6ea51838c14680a Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Mon, 15 Jul 2019 15:41:33 -0400 Subject: [PATCH 2/2] Correct uWSGI socket path in nginx/Apache docs --- doc/source/admin/apache.md | 2 +- doc/source/admin/nginx.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/admin/apache.md b/doc/source/admin/apache.md index 9e32e2d4613..57969815d97 100644 --- a/doc/source/admin/apache.md +++ b/doc/source/admin/apache.md @@ -228,7 +228,7 @@ previous section: ```yaml uwsgi: #... - socket: unix:///srv/galaxy/var/uwsgi.sock + socket: /srv/galaxy/var/uwsgi.sock mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app() manage-script-name: true # `module` MUST NOT be set when `mount` is in use diff --git a/doc/source/admin/nginx.md b/doc/source/admin/nginx.md index 488c9ce0a08..f73f98a9f67 100644 --- a/doc/source/admin/nginx.md +++ b/doc/source/admin/nginx.md @@ -220,7 +220,7 @@ previous section: ```yaml uwsgi: #... - socket: unix:///srv/galaxy/var/uwsgi.sock + socket: /srv/galaxy/var/uwsgi.sock mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app() manage-script-name: true # `module` MUST NOT be set when `mount` is in use