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GitHub is where the world builds software. Millions of developers and companies build, ship, and maintain their software on GitHub — the largest and most advanced development platform in the world. Added support for 4.76 CEX/DEX and 4.78 CEX/DEX (thanks @Ps3itaTeam) Updated code database to Bungholio's April 28th, 2016 update (thanks Bungholio) Artemis packages will now be held in the releases tab of the GitHub. 21.0.6.1 start.runs(model). This code starts the model runs using a model specific run function named start.runs.model.If the ecosystem model is running on a remote server, this module also takes care of all of the communication with the remote server and its run queue. PowerPC and Solaris Support: Due to lack of demand at IPAC, active SciApps support for PowerPC Macs (macosx) was frozen in the Doctor Orpheus (March 2010) release. Future SciApps updates for Mac OS X will not include updates to macosx software, and the macosx distribution will disappear entirely during a future Mac OS X SciApps update (late 2011 or early 2012).

Home Artemis ACT BamView DNAPlotter

Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.Full information about the latest release of Artemis can be found in the Artemis manual.

The Artemis poster gives an overview of browsing genomes and visualisation of next generation data in Artemis.

Then gunzip gcc-10.2-bin.tar.gz (if your browser didn't do so already) and then sudo tar -xvf gcc-10.2-bin.tar -C /. It installs everything in /usr/local. You can invoke the Fortran 95 compiler by simply typing gfortran. Welcome; I Introduction; 1 Project Overview; 2 Contributor Covenant Code of Conduct; 3 About the PEcAn Book. 3.0.1 Main Topics; 3.1 How to Contribute.

Publication

High-throughput sequencing (HTS) technologies have made low-cost sequencing of large numbers of samples commonplace. An explosion in the type, not just number, of sequencing experiments has also taken place including genome re-sequencing, population-scale variation detection, whole transcriptome sequencing and genome-wide analysis of protein-bound nucleic acids.We present Artemis as a tool for integrated visualization and computational analysis of different types of HTS datasets in the context of a reference genome and its corresponding annotation.

If you make use of this software in your research, please cite as:

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.
Carver T, Harris SR, Berriman M, Parkhill J and McQuillan JA
Bioinformatics (Oxford, England) 2012;28;4;464-9
PUBMED: 22199388; PMC: 3278759; DOI: 10.1093/bioinformatics/btr703

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.
Carver T, Berriman M, Tivey A, Patel C, Böhme U et al.
Bioinformatics (Oxford, England) 2008;24;23;2672-6
PUBMED: 18845581; PMC: 2606163; DOI: 10.1093/bioinformatics/btn529

Viewing and annotating sequence data with Artemis.
Berriman M and Rutherford K
Briefings in bioinformatics 2003;4;2;124-32
PUBMED: 12846394

Artemis: sequence visualization and annotation.
Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA and Barrell B
Bioinformatics (Oxford, England) 2000;16;10;944-5 PUBMED: 11120685

Software Availability

The Artemis Software is available under GPL3. The source code can be found on GitHub.

The latest release of Artemis can be downloaded by clicking on the relevant link below:

Or via Bioconda. Simply use:

from the command line, and you’re ready to go (no Java installation required).

For older versions of the software please see the Artemis FTP site

The old v17.0.1 version of the Artemis software required Java version 1.8 to run. All recent releases from v18.0.0 onwards require a minimum of Java 9 and ideally Java 11. This must be installed first. The easiest way to install a non-commercial open source Java version is from AdoptOpenJDK - just select the OpenJDK version and Hotspot options for the relevant platform. See the user manual for further options. A Java installation is not required for the Bioconda or Docker options.

Installation

For UNIX/Linux

Change directory to the directory you wish to install the Artemis software in. We will use ~/ in this example and in the next chapter.

Uncompress and untar the artemis-unix-release-{version}.tar.gz or artemis-unix-release-{version}.zip file. On UNIX the command is:

This will create a directory called ~/artemis which will contain all the files necessary for running Artemis and the other tools.

For MacOSX

For MacOSX users, an artemis-macosx-release-{version}.dmg.gz disk image is provided. Double-click on this file in your Downloads folder to unzip it. Then double-click the unzipped artemis-macosx-release-{version}.dmg to mount the “Artemis_Tools” image and display its contents - the Artemis, ACT, BamView and DNAPlotter applications. These apps can then be dragged to any desired location, for example, your dock or desktop. The download file can be unzipped from the command line using gunzip, if necessary:

There’s also an artemis-macosx-chado-release-{version}.dmg disk image that will start up Artemis with a Chado connection window displayed, if you wish to work connected to a Chado database in Artemis or ACT. This is installed in exactly the same way.

If you wish to run Artemis from the command line instead, then a script is provided within the app package to do this:

For Windows

Copy the artemis-windows-release-{version}.zip file to the directory that you wish to install to and then unzip using an application such as WinZip.This should unpack the artemis.jar, act.jar, bamview.jar and dnaplotter.jar application files.

Usage

Running Artemis on UNIX/Linux Systems

The easiest way to run the program is to run the script called art in the Artemis installation directory, like this:

Alternatively you can start Artemis with the name of a sequence file or embl file, eg:

For other available options use:

Running Artemis on Macintosh Systems

On MacOSX machines, Artemis can be started by double clicking on the Artemis icon.To start with a sequence file pre-loaded, simply drag the file on top of the Artemis icon.

You may find that when trying to run the Artemis app for the first time, that you get a security warning window displayed stating that “the application cannot be opened because it is from an unidentified developer” (because the apps are not obtained from the app store). If that’s the case, then just okay the window. Go into your System Preferences via the apple symbol at top left of screen. Then select “Security and Privacy”. You should then see a button called “Open Anyway”, next to some text saying “Artemis was blocked from opening because it is not from an identified developer”. Click on the “Open Anyway” button, which will then display the security warning window again - click the “Open” button on it and Artemis should then start. The application will then open straight away after this, without any further security warnings.

Running Artemis on Windows Systems

Artemis can be started by double clicking on the artemis.jar icon.

Running ACT via Bioconda

The Artemis start script is available in the path, so in a terminal window just use:

The User Manual

For additional information please see the Artemis manual and our GitHub page. A PDF version of the manual is also available for download here.

Some notes on Chado access can also be found here.

Contact

For issues encountered with installing the software please contact your local system administrator. For all other issues, please report them to our Github issues page or email artemis-help@sanger.ac.uk.

FAQ

Why does Artemis run out of memory on UNIX or GNU/Linux even though the machine has lots of memory?

The Java Virtual Machine (JVM) on UNIX has a fixed upper limit on the amount of memory that is available for applications, but this limit can be changed at runtime. As shipped Artemis will use a maximum of 2GB of memory.

There are two ways of fixing this problem:

Change the art script. Find the line that reads: FLAGS=”-mx2g -ms100m -noverify” and change the 2g (2 gigabytes) to a bigger number dependent on your machine memory (try 3g), or
Create an ARTEMIS_JVM_FLAGS environment variable set to “-mx2g -ms100m”, adjusting the mx value as required. No script change is required for this, but it would need to be added to your environment.

Why does Artemis run out of memory on MacOSX even though the machine has lots of memory?

To change the memory allocated to Artemis on MacOSX, set the value in the file Info.plist in the directory Artemis.app/Contents. Towards the bottom of the file you will see these lines:

Changing the value after -mx will change the max memory used by Artemis. The default is 2Gb.

Why does Artemis run out of memory on Windows even though the machine has lots of memory?

Normally the Java virtual machine artificially limits the amount of memory that Artemis can use. The fix is as follows:

Create a shortcut to the artemis.jar JAR file. Edit the properties of the shortcut and add java -mx2g -jar to the start of the Target: field. -mx2g sets the maximum memory Java will allocate to Artemis (2 gigabytes in this case). We recommend choosing a number that is about 50 megabytes less than the total amount of memory in the machine (to allow for the overhead of windows and the Java virtual machine).

You will need to use the shortcut to run Artemis from then on.

This chapter provides the following information for each release:

A link to the full release notes which includes all issues resolved in the release.
A brief list of 'highlights' when applicable.
If necessary, specific steps required when upgrading from the previous version.
- Note: If the upgrade spans multiple versions then the steps from each version need to be followed in order.
- Note: Follow the general upgrade procedure outlined in the Upgrading the Broker chapter in addition to any version-specific upgrade instructions outlined here.

2.14.0

Full release notes.

Highlights:

Management methods to update diverts
Ability to 'disabled' a queue so that messages are not routed to it
Support JVM GC & thread metrics
Support for resetting queue properties by unsetting them in broker.xml
Undeploy diverts by removing them from broker.xml
Add addressMemoryUsagePercentage and addressSize as metrics

Upgrading from older versions

Make sure the existing queues have their parameters set according to the broker.xml values before upgrading.

2.13.0

Full release notes.

Highlights:

Management methods for an address' duplicate ID cache to check the cache's size and clear it
Support for min/max expiry-delay
Command-line check tool for checking the health of a broker
Support disabling metrics per address via the enable-metrics address setting
Improvements to the audit logging
Speed optimizations for the HierarchicalObjectRepository, an internal object used to store address and security settings

Upgrading from older versions

Version 2.13.0 added new audit loggingwhich is logged at INFO level and can be very verbose. Thelogging.properties shipped with this new version is set up to filter this outby default. If your logging.properties isn't updated appropriately this auditlogging will likely appear in your console and artemis.log file assumingyou're using a logging configuration close to the default. Add this to yourlogging.properties:

2.12.0

Full release notes.

Highlights:

Support for SOCKS proxy
Real large message support for AMQP
Automatic creation of dead-letter resources akin to ActiveMQ 5's individual dead-letter strategy
Improved API for queue creation
Allow users to override JAVA_ARGS via environment variable
Reduce heap usage during journal loading during broker start-up
Allow server header in STOMP CONNECTED frame to be disabled
Support disk store used percentage as an exportable metric (e.g. to be monitored by tools like Prometheus, etc.)
Ability to configure a 'customizer' for the embedded web server
Improved logging for errors when starting an acceptor to more easily identify the acceptor which has the problem.
The CLI will now read the broker.xml to find the default connector URL for commands which require it (e.g. consumer, producer, etc.)

2.11.0

Full release notes.

Highlights:

Support retroactive addresses.
Support downstream federated queues and addresses.
Make security manager configurable via XML.
Support pluggable SSL TrustManagerFactory.
Add plugin support for federated queues/addresses.
Support com.sun.jndi.ldap.read.timeout in LDAPLoginModule.

2.10.0

Full release notes.

This was mainly a bug-fix release with a notable dependency change impacting version upgrade.

Upgrading from 2.9.0

Due to the WildFly dependency upgrade the broker start scripts/configuration need to be adjusted after upgrading.

On *nix

Locate this statement in bin/artemis:

This needs to be replaced with this:

On Windows

Locate this part of JAVA_ARGS in etc/artemis.profile.cmd respectively bin/artemis-service.xml:

This needs to be replaced with this:

2.9.0

Full release notes.

This was a light release. It included a handful of bug fixes, a few improvements, and one major new feature.

Highlights:

Support exporting metrics.

2.8.1

Full release notes.

This was mainly a bug-fix release with a notable dependency change impacting version upgrade.

Upgrading from 2.8.0

Due to the dependency upgrade made on ARTEMIS-2319 thebroker start scripts need to be adjusted after upgrading.

On *nix

Locate this if statement in bin/artemis:

This needs to be replaced with this block:

Notice that the jboss-logmanager version has changed and there is also a new wildfly-common library.

Not much further down there is this line:

This line should be changed to be: