From 8b13fe58bf6a696f9dfb10c26133ecd184dc1f22 Mon Sep 17 00:00:00 2001 From: Peter Briggs Date: Tue, 14 Jul 2020 09:52:59 +0100 Subject: [PATCH 1/2] Documentation: minor update to the README. --- README.rst | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.rst b/README.rst index 6417620..958f8af 100644 --- a/README.rst +++ b/README.rst @@ -58,6 +58,12 @@ instances. Nebulizer Basics ---------------- +Generally Nebulizer commands take the form: + +:: + + nebulizer COMMAND GALAXY [OPTIONS] + To interact remotely with a Galaxy instance using Nebulizer requires at minimum the URL of the instance and then either an API key or a user login name. From c9f47899d807d26edfc040dac764839dcbcdf282 Mon Sep 17 00:00:00 2001 From: Peter Briggs Date: Tue, 14 Jul 2020 09:53:45 +0100 Subject: [PATCH 2/2] Documentation: some tweaks to the tutorial. --- docs/tutorial.rst | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/docs/tutorial.rst b/docs/tutorial.rst index 2df1f9a..f898ba1 100644 --- a/docs/tutorial.rst +++ b/docs/tutorial.rst @@ -76,7 +76,7 @@ web browser to http://127.0.0.1:8080/ Finally you will need to register an account in Galaxy with the same email address as the one used for -``admin_users`` (for example ``admin@localhost.org``), +``admin_users`` (``admin@localhost.org`` in this example), using the web browser. Now you're ready to run through the tutorial. @@ -90,9 +90,8 @@ Now you're ready to run through the tutorial. 1. Install Nebulizer -------------------- -First you need to install a copy of Nebulizer, which -is best done in a Python virtual environment - for -example: +Installing Nebulizer is best done in a Python virtual +environment - for example: :: @@ -109,7 +108,7 @@ example: Once this is done you should have access to the ``nebulizer`` utility. -To list the available commands do: +To list the available commands: :: @@ -165,9 +164,9 @@ or Galaxy API key on the command line. For example: .. warning:: - This won't work if you didn't make register an - account ``admin@localhost.org`` when preparing the - local Galaxy! + This won't work if you didn't make an account + for ``admin@localhost.org`` when preparing the + local Galaxy in the previous step! This is quite laborious when executing several commands, so Nebulizer allows you to associate Galaxy instances and @@ -433,14 +432,15 @@ repository is also installed: * fastqc toolshed.g2.bx.psu.edu devteam 21:e7b2202befea Installed U trimmomatic toolshed.g2.bx.psu.edu pjbriggs 12:51b771646466 Installed -Here ``U`` indicates there is a major newer version -available. +Here ``U`` indicates there is a newer revision available +with a new version of the tool (``u`` indicates a newer +revision without a tool version update). Rerunning the ``list_installed_tools`` command with the ``--updateable`` option filters the list of tool repositories to just those with available updates. -We can update Trimmomatic to the newer version automatically +We can update Trimmomatic to the newest version automatically by running the ``update_tool`` command: ::