X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fcommandline.html;h=381478f0d7358e6f7a6a112abbd3937d2abaec1e;hb=d5bd34eb49f43735e240058f8875ab0bfcae4441;hp=0159a9220e39645813464f559bd3ce7aab2e5c38;hpb=dd0aacc45f9b0afb9031b0808797961e05a42b5d;p=jalview.git diff --git a/help/help/html/features/commandline.html b/help/help/html/features/commandline.html index 0159a92..381478f 100644 --- a/help/help/html/features/commandline.html +++ b/help/help/html/features/commandline.html @@ -28,32 +28,52 @@
Jalview can be run from the command line, and provides a range of arguments. These arguments - can also be passed via .JVL files, which are opened - automatically by the Jalview application when double-clicked in a - file browser on Windows and OSX. + href="clarguments.html">range of arguments.
- -From version 2.11.2, Jalview includes a launching shell script which is the recommended way to - launch an installed Jalview application from the command line. It supports all the command line arguments - that Jalview has previously supported, but makes it easier to launch directly from the command line.
+There are a few different ways to do this:
++ Jalview's command line launch + script +
Since version 2.11.2, the Jalview native application includes a launching shell script. This is the easiest way to + launch an installed Jalview application from the command line.
To run the launch script, simply open a Terminal (or Command prompt on Windows), and type:
+ jalview+
There are some important differences between the using the launching script and launching Jalview from its icon: +
+ If typing 'jalview' in the terminal prompt (or windows command line)
+ doesn't work then you will need to add the location of the jalview
+ launch script to your
+ PATH
.
+ How you do this depends on your operating system.
- -If you installed Jalview prior to version 2.11.2 you will not have had the option to add the launching shell script to your PATH.
- If your application has updated to 2.11.2 then the scripts will now be there, but not in your PATH
.
- There are instructions below to add the launching shell script to your PATH
if you want to do so.
In Linux or Unix (jalview.sh
)
The installer gives you the option of adding a symbolic link to +
Running the Linux installer will give you the option of adding a symbolic link to
that script in your $PATH
, if it finds a suitable place that your user can add such a
link (e.g. ~/bin
, ~/.local/bin
, ~/local/bin
, ~/opt/bin
). If you chose that option then
you should be able to launch Jalview on the command line with the simple command
@@ -66,7 +86,7 @@
In Windows (jalview.bat
, jalview.ps1
)
The installer gives you the option of adding Jalview's script folder to your %PATH%
allowing you to launch Jalview
+
The Windows installer will give you the option of adding Jalview's script folder to your %PATH%
allowing you to launch Jalview
in a Command Prompt simply with the command
jalviewIf you didn't choose that option during installation (or used an earlier version installer), you can either @@ -89,25 +109,37 @@
In macOS (jalview
)
- The script you should use to launch Jalview is linked to as -
/Applications/Jalview.app/Contents/MacOS/jalview- so you can run that command with its full path, or make your own symbolic link to there, or add that folder to your
$PATH
.
-
-
- If Jalview automatically updated from a version before 2.11.2 you will have to make a symbolic link to /Applications/Jalview.app/Content/Resources/app/bin/jalview.sh
with the command
-
ln -s /Applications/Jalview.app/Content/Resources/app/bin/jalview.sh jalview- -
Future
+We don't currently provide a macOS installer program, so you + will need to add the command to you path manually. The script you + should use to launch Jalview is linked to as +
/Applications/Jalview.app/Contents/MacOS/jalviewso you + can run that command with its full path, or make your own symbolic + link to there, or add that folder to your
$PATH
. echo /Applications/Jalview.app/Contents/Resources/app/bin | sudo tee -a /etc/paths.d/Jalview+ This adds the directory + "/Applications/Jalview.app/Contents/Resources/app/bin/" + to a "Jalview" file in the /etc/paths.d/ directory. The + lines from all the files in this directory are added the $PATH + variable for all shells and users. + +
+ If you cannot see the
+ jalview
+ command in the MacOS directory, then you probably have an older
+ Jalview installation. In that case, you should make a symbolic link
+ directly to the launch script with the command
+
ln -s /Applications/Jalview.app/Content/Resources/app/bin/jalview.sh jalview+ If this doens't work, check your installation is running + Jalview 2.11.2.0 or later. + +
If you are using a version of Jalview prior to 2.11.2, you can still launch from the command line, but you will have to @@ -122,7 +154,7 @@
open /Applications/Jalview.app --args -open /FULL/PATH/TO/myalignment.fa- (put all the Jalview arguments after the --args parameter, and note that paths to files should be full paths from
/
)
+ (put all the Jalview arguments after the --args parameter, and note that all files must be specified with their full paths)