Difference between revisions of "Downloads"

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[http://dx.doi.org/10.1109/TCBB.2016.2527647 Dias, O., Gomes, D., Vilaca, P., Cardoso, J., Rocha, M., Ferreira, E., & Rocha, I. (2016). Genome-wide Semi-automated Annotation of Transporter Systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics / IEEE, ACM, (1), 1–1. http://doi.org/10.1109/TCBB.2016.2527647]
 
[http://dx.doi.org/10.1109/TCBB.2016.2527647 Dias, O., Gomes, D., Vilaca, P., Cardoso, J., Rocha, M., Ferreira, E., & Rocha, I. (2016). Genome-wide Semi-automated Annotation of Transporter Systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics / IEEE, ACM, (1), 1–1. http://doi.org/10.1109/TCBB.2016.2527647]
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==Contacts==
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*Any bugs or suggestions please email us at:
 +
**support@merlin-sysbio.org'''
  
 
==Downloads==
 
==Downloads==
  
 
'''''merlin''''' is available for download in a single multi-platform version.
 
'''''merlin''''' is available for download in a single multi-platform version.
* ''merlin 3.6.1 beta'' is now available for download.
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** [https://merlin-sysbio.org/files/changelog.txt merlin.zip]
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* ''merlin 4.0.5 - beta'' - ''NEW'' (12/10/2020)
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** [https://www.merlin-sysbio.org/data/releases/merlin-gui-4.0.5-RELEASE-beta.zip merlin]
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 +
 
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'''Previous versions'''
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 +
* ''merlin 4.0.2 - beta''
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** [https://www.merlin-sysbio.org/data/releases/merlin-gui-4.0.2-RELEASE-beta.zip merlin]
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* ''merlin 4.0.3 - beta'' - (27/05/2020)
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** [https://www.merlin-sysbio.org/data/releases/merlin-gui-4.0.3-RELEASE-beta.zip merlin]
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* ''merlin 4.0.4 - beta'' - (06/07/2020)
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** [https://www.merlin-sysbio.org/data/releases/merlin-gui-4.0.4-RELEASE-beta.zip merlin]
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==Known issues==
 +
 
 +
* ''' I updated a plugin using the ''merlin'' plugin manager and now my version is unstable with several errors, how can I fix this ?'''
 +
** ''' Step 1 ''' - Run and close ''merlin'' twice. This is necessary for ''merlin'' to automatically identify and remove older versions of plugins and libraries.
 +
** ''' Verification ''' - To make sure that ''merlin'' is updated and functional, open your "lib" folder within your ''merlin'' directory and search for "merlin-*.jar" files (* meaning the multiple libraries). If there are duplicate libraries (where one is the older version and the other is the most recent one) please run ''merlin'' and close it after booting to the initial menu.
 +
 
 +
 
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* Plugin '''''merlin'''''-addons installed prior to version 4.0.2 might stop '''''merlin''''''s launch after an update. To solve this issue, please delete the file merlin-addons*.jar from directory [merlin_home]/plugins_bin. After completing this step, '''''merlin''''' should launch normally.
 +
 
 +
 
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* '''How can I recover my workspaces if ''merlin'' does not launch?'''
 +
** '''Step 1 -''' Download the latest version available in this page. Do not launch ''merlin'' until step 4.
 +
** '''Step 2 -''' Copy the directories [merlin_home]/h2Database and [merlin_home]/ws from your previous ''merlin'' version.
 +
** '''Step 3 -''' Paste both directories in ''merlin''´s version downloaded from the website. These directories should not exist if ''merlin'' was not launched yet.
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** '''Step 4 -''' Launch ''merlin''. All workspaces should be available now.
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 +
 
 +
We are currently working hard on finding a solution for these issues and we shall release a more stable version soon. Thank you for your patience!
  
 
==System requirements==
 
==System requirements==
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* ''Memory:'' 1GB memory (most operations use less than 1GB, however the local alignments may take up to 3GB)
 
* ''Memory:'' 1GB memory (most operations use less than 1GB, however the local alignments may take up to 3GB)
  
* ''OS:'' Windows (XP or later), Linux (Tested on Ubuntu Precise Pangolin)
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* ''Java version:'' above JRE 1.8 
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** ''Discalimer:'' more recent versions of Java (above 10) may cause stability issues
  
* Database:
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* ''OS:'' Windows (XP or later), Unix (Ubuntu or macOS),
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<!--* Database: I (DAVIDE) DID NOT PUT HIBERNATE HERE BECAUSE IS NOT A REQUIREMENT
 
** ''H2'': embedded database available
 
** ''H2'': embedded database available
** ''MySQL:'' alternatively a MySQL Server can be used
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** ''MySQL:'' alternatively a MySQL Server can be used-->
  
* If you want to upload your previous workspace to the new version of ''merlin'', please contact us at:
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<!--* If you want to upload your previous workspace to the new version of ''merlin'', please contact us at:
** support@merlin-sysbio.org
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** support@merlin-sysbio.org-->
  
 
==Changelog==
 
==Changelog==
*Any bugs or suggestions please email us at:
+
 
**support@merlin-sysbio.org'''
+
* Changelog history
* ''Latest update: 2018-04-27'' '''NEW RELEASE 3.6.1
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** [https://www.merlin-sysbio.org/files/changelog.txt changelog]
** change 1 (e.g. debugged Enzymes BLAST)
 
** change 2
 
** etc
 
* Previous changelogs
 
** [https://merlin-sysbio.org/files/changelog.txt changelog]
 
  
 
----
 
----
  
 
<div style="font-size:88%; line-height: 1.3em; " align="right">Application icons: https://www.flaticon.com</div>
 
<div style="font-size:88%; line-height: 1.3em; " align="right">Application icons: https://www.flaticon.com</div>

Latest revision as of 10:45, 12 October 2020

Please cite using

Dias, O., Rocha, M., Ferreira, E.C. and Rocha, I. (2015) Reconstructing genome-scale metabolic models with merlin. Nucleic Acids Res., 10.1093/nar/gkv294.

Dias, O., Gomes, D., Vilaca, P., Cardoso, J., Rocha, M., Ferreira, E., & Rocha, I. (2016). Genome-wide Semi-automated Annotation of Transporter Systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics / IEEE, ACM, (1), 1–1. http://doi.org/10.1109/TCBB.2016.2527647

Contacts

  • Any bugs or suggestions please email us at:
    • support@merlin-sysbio.org

Downloads

merlin is available for download in a single multi-platform version.

  • merlin 4.0.5 - beta - NEW (12/10/2020)


Previous versions

  • merlin 4.0.3 - beta - (27/05/2020)
  • merlin 4.0.4 - beta - (06/07/2020)

Known issues

  • I updated a plugin using the merlin plugin manager and now my version is unstable with several errors, how can I fix this ?
    • Step 1 - Run and close merlin twice. This is necessary for merlin to automatically identify and remove older versions of plugins and libraries.
    • Verification - To make sure that merlin is updated and functional, open your "lib" folder within your merlin directory and search for "merlin-*.jar" files (* meaning the multiple libraries). If there are duplicate libraries (where one is the older version and the other is the most recent one) please run merlin and close it after booting to the initial menu.


  • Plugin merlin-addons installed prior to version 4.0.2 might stop merlin's launch after an update. To solve this issue, please delete the file merlin-addons*.jar from directory [merlin_home]/plugins_bin. After completing this step, merlin should launch normally.


  • How can I recover my workspaces if merlin does not launch?
    • Step 1 - Download the latest version available in this page. Do not launch merlin until step 4.
    • Step 2 - Copy the directories [merlin_home]/h2Database and [merlin_home]/ws from your previous merlin version.
    • Step 3 - Paste both directories in merlin´s version downloaded from the website. These directories should not exist if merlin was not launched yet.
    • Step 4 - Launch merlin. All workspaces should be available now.


We are currently working hard on finding a solution for these issues and we shall release a more stable version soon. Thank you for your patience!

System requirements

The current version of merlin requires:

  • Processor: Reasonably powerful x64 hardware. Any recent Intel or AMD processor should do.
  • Memory: 1GB memory (most operations use less than 1GB, however the local alignments may take up to 3GB)
  • Java version: above JRE 1.8
    • Discalimer: more recent versions of Java (above 10) may cause stability issues
  • OS: Windows (XP or later), Unix (Ubuntu or macOS),


Changelog


Application icons: https://www.flaticon.com