Jalview Command Line Arguments

+ From version 2.11.3.0 Jalview has a new set of command line arguments + which allow more powerful and flexible combinations of arguments, though can + also be used for simple use cases too. +

+ These new arguments are all accessed with a ‑‑doubledash form of + command line argument (with the one exception where simply opening one or more + files can be performed without any arguments other than the filenames). +

+ The old command line arguments can still be used (see + the old page on command line arguments) so + existing scripts utilising them should not break. +
+ These are now deprecated and will be removed in a future version of Jalview. +

- The Jalview Executable's Command Line Arguments + However, you cannot mix old and new style arguments, so if you use any + -singledash arguments (with the exception of -help or -h), they will all be interpreted as + old style arguments with the new ‑‑doubledash + arguments being ignored. If you have a script + that uses the old arguments without any dashes, and uses the bare-word + open then these will also be interpreted as old style arguments.

+ Warning! If you use command line arguments without any dashes and + don't use the bare-word argument open then all + your arguments will be interpreted as alignment files to be opened by the + new command line argument process! +

Syntax

+ The new command line argument parser can group certain labelled arguments together, or give them a default label based on their position in the list of arguments (in which case you won't ever need to know what the label is). All arguments are read before any alignment actions are performed. For basic usage without additional syntax, please see the Command Line: basic usage explanatory page. +

+ Parts of Jalview's command line arguments +

+ Different arguments can take one or more values, others take no value and act like a switch (some can be set on and off and others are only on, depending on the use). +
+

+ This may sound complicated, but nearly everything can be done just with plain command line arguments (see Command Line: basic usage), though in this case the ordering of the arguments is more important. +

Headless mode

+ Jalview can be run in headless mode, i.e. without the usual graphical user interface (GUI), by specifying the ‑‑headless argument. With command line arguments you can specify operations for Jalview to perform on one or more files and then stop running. Most likely you will want to output another file, either an alignment for image file. +

+ If you specify an argument for an output file (one or more of ‑‑output, ‑‑image or ‑‑structureimage) then it will be assumed that you wish to run in headless mode. +

+ You can force Jalview to run in graphical mode using the ‑‑gui argument. +

-nodisplay

Run Jalview without - User Interface. (automatically disables questionnaire, version - and usage stats checks)

-open FILE/URL

Specify the alignment file to - open or process by providing additional arguments.

-props FILE/URL

Use the given Jalview properties - file instead of users default.

-features FILE/URL

- Use the given file to add sequence features to an alignment. - See Features - File (Known as Groups file prior to 2.08) description. -

-colour COLOURSCHEME

Set the colourscheme for the alignment. This can be any - of the built-in colourschemes, a name of a predefined - colourscheme (defined in the Jalview properties file), or an - 'inline' colourscheme (see the applet's colour parameter for - more information).

-annotations FILE/URL

Add precalculated annotations to the alignment. See Annotation - File description. -

-tree FILE/URL

Load the given newick format tree file - onto the alignment

-questionnaire URL

Queries the given URL for information - about any Jalview user questionnaires

-noquestionnaire

Turn off questionnaire check

-nonews

- Disable check for Jalview - news on startup (not recommended other than for classroom / - demo usage) -

-nousagestats

Turn off google analytics usage tracking

-[no]sortbytree

Enable or disable automatic sorting of - associated view when a new tree is displayed

-groovy FILE/URL

Execute groovy script in FILE (where - FILE may be 'STDIN' to read from the standard input) after all - other arguments have been processed

-jabaws URL

Specify the URL of the preferred JABAWS - server

-fasta FILE

Create alignment file FILE in Fasta - format.

-clustal FILE

Create alignment file FILE in - Clustal format.

-msf FILE

Create alignment file FILE in MSF - format.

-pileup FILE

Create alignment file FILE in - Pileup format.

-pir FILE

Create alignment file FILE in PIR - format.

-pfam FILE

Create alignment file FILE in - PFAM format.

-blc FILE

Create alignment file FILE in BLC - format.

-json FILE

Create alignment file FILE in - JSON format.

-jalview FILE

Create alignment file FILE in - Jalview format.

-png FILE

Create PNG image FILE from - alignment.

-imgMap FILE

Create HTML file FILE with image - map of PNG image.

-eps FILE

Create EPS file FILE from - alignment.

-svg FILE

Create Scalable Vector Graphics - file FILE from alignment.

-biojsMSA FILE

Write an HTML page to display - the alignment with the - BioJS MSAviewer MSA -

-jvmmempc=PERCENT

Only available with standalone executable jar or jalview.bin.Launcher. - Limit maximum heap size (memory) to PERCENT% of total physical memory detected. - This defaults to 90 if total physical memory can be detected. - See Memory usage settings for Jalview for more details. -

-jvmmemmax=MAXMEMORY

Only available with standalone executable jar or jalview.bin.Launcher. - Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), - gigabytes(g) or if you're lucky enough, terabytes(t). - This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. - See Memory usage settings for Jalview for more details. -

Command Line: introduction and reference

Introduction

Syntax

+ Parts of Jalview's command line arguments +

Headless mode