chipster-announcements Mailing List for Chipster analysis software

Hello,

this message affects only those who have installed their own Chipster server. Chipster end-users using for example the Chipster in https://chipster.csc.fi can ignore this message.

Our server installation instructions used to tell that we are going inform about important security vulnerabilites on this chipster-announcements email list. We have now noticed that this is impractical and it would be better to separate the information for end-users and server maintainers. From now on this chipster-announcements list will focus on the information that is relevant for end-users, e.g. information about new analysis features. Communication for Chipster server maintainers will move to chipster-tech list. 

If you maintain a Chipster server or are interested in technical discussion regarding Chipster, please subscribe to chipster-tech list in https://chipster.rahtiapp.fi/contact . The page contains also link to the old messages, in case you missed the message today about the log4j vulnerability.

Best regards,
Petri / Chipster team

Dear all, 

Please note that the virtual machine image of Chipster v3.16.3 is now available for download at [ http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/build/3.16.3/ | http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/build/3.16.3/ ] . Should you have any problem updating your Chipster server to this version, please don't hesitate to contact us. This version brings major improvements if compared to Chipster v3.15: 
-all the single cell RNA-seq analysis tools have been migrated to Seurat v3 and R3.6.1 
-a bug in HISAT2 aligners affecting downstream analysis with Cufflinks and Cuffdiff has been fixed (please refer your users to [ https://chipster.csc.fi/manual/newVersion.html | https://chipster.csc.fi/manual/newVersion.html ] for details) 

Best, 
Eija and the Chipster team 



Eija Korpelainen, Ph.D 
Product Manager 


CSC - IT Centre for Science 
P.O.Box 405, 02101 Espoo, Finland 
Phone +358 50 381 9726 

Hi all,

We are happy to announce that the virtual machine images for Chipster v3.15 are released. Please find the images at http://bio.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/build/3.15.0/.

In this release the Chipster client jar is signed with a new certificate, which is valid again for the next three years. Please see the release notes at http://chipster.csc.fi/manual/newVersion.html for other changes.

Should you have any trouble, please don't hesitate to email 
chi...@li....
 
Best regards,
Petri and the rest of the team

Dear all,

Chipster 3.14.2 and older virtual machines contain a Chipster client jar file which is signed by a certificate which expires 1st of May 2019. This means that after this date when starting the Chipster client, Java Web start will complain about expired certificate.

You can fix an existing Chipster virtual machine installation by replacing the client jar file with a new file which has been signed with a new certificate. This can be done by running the following steps:

1) Log in to the chipster virtual machine as user chipster 
2) cd /opt/chipster/webstart/web-root/lib
3) mv chipster-current.jar chipster-current-backup.jar
4) wget http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/patches/3.14.2/chipster-current.jar

If you are still running Chipster 3.12.3, replace 3.14.2 with 3.12.3 in step 4)

Chipster 3.15 virtual machine images which also have this issue fixed will be available soon.

Sorry for the rather late notice,

	Chipster Team

Dear all,

A last minute change in the Chipster 3.11.1 caused a bug which prevented tools from writing result files and incorrectly complained about insufficient disk space. This is fixed the Chipster 3.11.2. The new images are available at

    http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/3.11.2/

Or ff you have already installed the previous version 3.11.1, you can update your VM simply by running the update script:

    https://github.com/chipster/chipster/wiki/TechnicalManual#upgrading-vm-bundled-installation

Sorry for the inconvenience!

Best regards,
Petri and the Chipster team


> On 11 Jan 2017, at 10:57, chi...@cs... wrote:
> 
> Dear all,
> 
> We are happy to announce that the virtual machine images for Chipster v3.11 are finally released, thank you for your patience! Please find the images at http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/3.11.1/.
> 
> We strongly encourage you to update your local Chipster servers to this version, as it contains many improvements, including the following (for a full list, please see the release notes for v3.9-3.11 at http://chipster.csc.fi/manual/newVersion.html):
> -Ubuntu has been updated to v16.4
> -reference data and analysis tools have been updated to new versions
> -many analysis tools have been improved
> -many new analysis tools have been added (including tools for single cell RNA-seq data and a virus detection pipeline for small RNA-seq data)
> 
> Wishing you a Happy New Year,
> Eija and the Chipster team
> 
> ------------------------------------------------------------------------------
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today. http://sdm.link/xeonphi_______________________________________________
> Chipster-tech mailing list
> Chi...@li...
> https://lists.sourceforge.net/lists/listinfo/chipster-tech

Dear all, 

We are happy to announce that the virtual machine images for Chipster v3.11 are finally released, thank you for your patience! Please find the images at http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/3.11.1/. 

We strongly encourage you to update your local Chipster servers to this version, as it contains many improvements, including the following (for a full list, please see the release notes for v3.9-3.11 at http://chipster.csc.fi/manual/newVersion.html): 
-Ubuntu has been updated to v16.4 
-reference data and analysis tools have been updated to new versions 
-many analysis tools have been improved 
-many new analysis tools have been added (including tools for single cell RNA-seq data and a virus detection pipeline for small RNA-seq data) 

Wishing you a Happy New Year, 
Eija and the Chipster team 

Dear all, 




Please note that a bug was discovered yesterday in the DESeq2 tool that caused the logFC to be reported the wrong way around in situations where there are more than 2 groups. This bug has been now fixed, and the virtual machine images for Chipster v3.8.1 containing the fix are available for download at http://chipster.github.io/chipster/. Please note that Chipster 3.8.0 can be easily updated to 3.8.1 from within the virtual machine by running ./update.sh in /opt/chipster. We are sorry for the hassle and thank Mari Häkkinen for reporting the problem! 




Best regards, 
Eija and the Chipster team 


Eija Korpelainen, Ph.D 
Product Manager 
Application services, Bioinformatics 
CSC - IT Centre for Science 
P.O.Box 405 
02101 Espoo, Finland 

Hi,

a small correction to this. You can use the update.sh script to update Chipster 3.7.0 and later to 3.8.0. For Chipster versions older than 3.7.0 you need to download the latest version from http://chipster.github.io/chipster.

Also, if you have previously used update.sh to update from 3.6.x to 3.7.x we recommend that you download the latest version from http://chipster.github.io/chipster. Some Ensembl genome data files may not have been updated correctly when updating from 3.6 to 3.7.

Were are sorry for any possible inconvenience.

Taavi and the Chipster team

--
Taavi Hupponen, Chipster Team
CSC. P.O.Box 405, 02101 ESPOO, Finland
tel. +358-9-4572283 fax. +358-9-4572302
CSC - IT Center for Science, http://www.csc.fi
email: taa...@cs...


> On 27 Apr 2016, at 13:18, Eija Korpelainen <eij...@cs...> wrote:
> 
> Hi all,
> 
> Please note that the virtual machine images for Chipster v3.8 are now available for download at http://chipster.github.io/chipster/. Importantly, the client jar file has been signed with a renewed certificate (the previous certificate had expired, which caused problems when launching Chipster in Mac OS X). Chipster 3.6.2 and later can be updated to 3.8 from within the virtual machine by running ./update.sh in /opt/chipster.
> 
> In addition to the improvements listed at http://chipster.csc.fi/manual/newVersion.html, this version contains a fix to the Cuffdiff bug that produced an error when the option "Correct for sequence-specific bias" was selected. Big thanks to Melanie Grobbelaar from the Stellenbosch University for spotting the bug!
> 
> 
> Best regards,
> Eija and the Chipster team
>  
> Eija Korpelainen, Ph.D
> Product Manager
> Application services, Bioinformatics
> CSC - IT Centre for Science
> P.O.Box 405
> 02101 Espoo, Finland
> ------------------------------------------------------------------------------
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> Chipster-announcements mailing list
> Chi...@li...
> https://lists.sourceforge.net/lists/listinfo/chipster-announcements

Hi all, 





Please note that the virtual machine images for Chipster v3.8 are now available for download at http://chipster.github.io/chipster/. Importantly, the client jar file has been signed with a renewed certificate (the previous certificate had expired, which caused problems when launching Chipster in Mac OS X). Chipster 3.6.2 and later can be updated to 3.8 from within the virtual machine by running ./update.sh in /opt/chipster. 




In addition to the improvements listed at http://chipster.csc.fi/manual/newVersion.html, this version contains a fix to the Cuffdiff bug that produced an error when the option "Correct for sequence-specific bias" was selected. Big thanks to Melanie Grobbelaar from the Stellenbosch University for spotting the bug! 







Best regards, 
Eija and the Chipster team 

Eija Korpelainen, Ph.D 
Product Manager 
Application services, Bioinformatics 
CSC - IT Centre for Science 
P.O.Box 405 
02101 Espoo, Finland 

Hi all, 


Please note that the virtual machine images for Chipster v3.7 are now available for download at http://chipster.github.io/chipster/. 

This version includes several improvements and updates as described at http://chipster.csc.fi/manual/newVersion.html, including a possibility to save analysis sessions on the server side. This cloud session feature is still experimental and therefore turned off by default. If you as a server admin would like to enable this functionality for your users, please read carefully the instructions for migration and backups at https://github.com/chipster/chipster/wiki/TechnicalManual#cloud-sessions . 

Best regards, 
Eija and the Chipster team 

Eija Korpelainen, Ph.D 
Product Manager 
Application services, Bioinformatics 
CSC - IT Centre for Science 
P.O.Box 405 
02101 Espoo, Finland 

Hi all, 


Please note that the virtual machine images for Chipster v3.6.3 are now available for download at http://chipster.github.io/chipster/. We recommend that you update your Chipster v3.4 server to this new version, because it contains some major improvements. Importantly, we have re-written the job manager component in Java, because the earlier Python based version caused random messaging errors, which showed as occasional problems when starting the Chipster client software. The new job manager has now been used in our national Chipster server for some months, and it seems to work reliably. Please find the full release notes including analysis tool updates at http://chipster.csc.fi/manual/newVersion.html. 

Wishing you all the best for 2016 from snowy Finland, 
Eija and the Chipster team 

Eija Korpelainen, Ph.D 
Product Manager 
Application services, Bioinformatics 
CSC - IT Centre for Science 
P.O.Box 405 
02101 Espoo, Finland 

Dear all, 

We are happy to announce that the version 3.4 of Chipster server environment is finally released. You can download the ready-to-run Ubuntu based virtual machine image from http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/3.4.0/. Please note that for this update you need to download the new image rather than running just the update script, because there are some major changes such as a new job manager component if compared to the 3.1 version that was available before. You can check out the new functionality in the release notes for Chipster versions 3.2, 3.3 and 3.4 at http://chipster.csc.fi/manual/newVersion.html. 

Best regards, 
Eija and the Chipster team 

Hi all,
 
We are happy to inform you that the Chipster v3.1 server environment is finally available for download at http://chipster.github.io/chipster/ . It contains major improvements to the Chipster server version v2.12 which was released in May. Please see the release notes for v3.0 and v3.1 at http://chipster.csc.fi/manual/newVersion.html .

The server environment is released as ready-to-run Ubuntu based virtual machine (VM) images and standalone server installation packages. 

Updating with update.sh script is not possible this time due to major changes made in this release. Download a new copy of the virtual machine instead. 

Should you have any trouble with the Chipster version update, please don't hesitate to email chi...@li... .

Best regards,
Petri and the rest of the team

Hi all,

Just a quick note to inform you that  

1. Registration for the international ChIP- and DNase-seq data analysis workshop is now open at http://www.csc.fi/english/csc/courses/archive/chipseq2014. The workshop covers several topics ranging from alignment and peak calling to motif detection and annotation. The program consists of a lecture day (18th of September), and several hands-on days that participants can choose from. This workshop is part of the FP7 AllBio project (http://www.allbioinformatics.eu), which kindly provides 15 travel bursaries of 500 euros for early stage researchers. The registration deadline is 21.8.2014.


2. We released today Chipster v3.0 (see release notes at http://chipster.csc.fi/manual/newVersion.html). We will first run it on our server for a week or two to make sure that everything is fine, and release then as a VM. In addition to new analysis tools it has major improvements to the user interface. If you would like to have a sneak preview, you can log in to our server (http://chipster.csc.fi/) with username guest.


Best regards,
Eija and the Chipster team


Eija Korpelainen, Ph.D
Product Manager
Application services, Bioinformatics
CSC - IT Centre for Science
P.O.Box 405, 02101 Espoo, Finland
Phone +358 50 381 9726

Hi all, 
  
We are happy to inform you that the Chipster v2.12 server environment is finally available for download at http://chipster.sourceforge.net/downloads.shtml . It contains major improvements to the Chipster server version v2.9 which was released in December. Please see the release notes for v2.12 and v2.11 at http://chipster.csc.fi/manual/newVersion.html . 

  

The server environment is released as ready-to-run Ubuntu based virtual machine (VM) images and standalone server installation packages. Please note that this VM may be incompatible with some VMware products. Please let us know if you using VMware, we would like to know how many users need an image for this platform. 

  

You can update to Chipster 2.12 from within the virtual machine using the update.sh script. This script will simplify and speed up the update process by downloading and installing only the changed files. The script is located in the /opt/chipster directory. Before running it you should stop all the Chipster services. Note that the update script is not able to install one library required for the png result files of EMBOSS tools. This is due to the imcompatible Ubuntu version, which will updated to Ubuntu 12.04 in the next release in about 6 weeks time. 

  

Should you have any trouble with the Chipster version update, please don't hesitate to email chi...@li... . 
  
  
Best regards, 
Eija and the rest of the team 
  
  
Eija Korpelainen, Ph.D 
Product Manager 
Application services, Bioinformatics 
CSC - IT Centre for Science 
P.O.Box 405 
02101 Espoo, Finland 

Hi all, 
  
We are happy to announce the release of Chipster v2.9, which contains many analysis tool updates and improvements to the genome browser. In order to made it easier for the developer community to integrate new analysis tools in Chipster, this new version provides a graphical tool editor environment and support for Python (for details, please see http://chipster.csc.fi/manual/newVersion.html ).  
  
For those running their own servers, Chipster 2.9 server environment is release d as ready-to-run Ubuntu based virtual machine images and standalone server installation packages. The packages are available at: 
http://chipster.sourceforge.net/downloads.shtml . You can update to Chipster 2.9 from within the virtual machine by using the update.sh script. This script will simplify and speed up the update process by only downloading and installing changed files. The script is located in the /opt/chipster directory. Before running it you should stop all the Chipster services. Should you have any trouble, please don't hesitate to email 
chi...@li... . 
  
  
Best regards, 
Eija and the rest of the team 
  
  
Eija Korpelainen, Ph.D 
Product Manager 
Application services, Bioinformatics 
CSC - IT Centre for Science 
P.O.Box 405, FIN-02101 Espoo, Finland 
Phone +358 50 381 9726 

Hi all, 
  
Please note that an update script is now available for updating your local Chipster server to version 2.8.1. The script replaces the RNA-seq aligner TopHat v2.0.4 with v2.0.9. This is important, because the older TopHat is not able to recognize the latest Bowtie2 (v2.1.0) that we included in Chipster 2.8.0 two weeks ago. The update script is available at http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/ . 
  
Best regards, 
Eija and the rest of the Chipster team 

Eija Korpelainen, Ph.D 
Product Manager 
Application services, Bioinformatics 
CSC - IT Centre for Science 
P.O.Box 405, FIN-02101 Espoo, Finland 
Phone +358 50 381 9726 
  

Hi all, 
  
We are happy to announce the release of Chipster v2.8.0, which contains many improvements to visualizations and some new analysis tools (for details, please see http://chipster.csc.fi/manual/newVersion.html ). Please note that this version requires Java 1.7, so check your Java version if you experience problems when launching Chipster. 
  
For those running their own servers, Chipster 2.8.0 server environment is release d as ready-to-run Ubuntu based virtual machine images and standalone server installation packages. The packages are available at: 
http://chipster.sourceforge.net/downloads.shtml 
You can update to Chipster 2.8.0 from within the virtual machine by using the update.sh script. This script will simplify and speed up the update process by only downloading and installing changed files. The script is located in the /opt/chipster directory. Before running it you should stop all the Chipster services. Should you have any trouble, please don't hesitate to email 
chi...@li... . 
  
Best regards, 
Eija and the rest of the team 
  
Eija Korpelainen, Ph.D 
Product Manager 
Application services, Bioinformatics 
CSC - IT Centre for Science 
P.O.Box 405, FIN-02101 Espoo, Finland 
Phone +358 50 381 9726 
  
  

Hello all,

We are happy to announce that version 2.7.0 of Chipster server
environment is released as ready-to-run Ubuntu based virtual machine
images and standalone server installation packages.

The packages are available at:
http://chipster.sourceforge.net/downloads.shtml

Release notes are available at:
http://chipster.sourceforge.net/release_notes.shtml

You can update to Chipster 2.7.0 from within the virtual machine by using the 
update.sh script. This script will simplify and speed up the update 
process by only downloading and installing changed files. The script is 
located in the /opt/chipster directory. Before running it you should 
stop all the Chipster services.

Should you have any trouble, don't hesitate to drop a mail at
chi...@li... (or contact us directly, if you wish).

Cheers,
Aleksi and the rest of the team

Hello all,

We are happy to announce that version 2.6.1 of Chipster server
environment is released as ready-to-run Ubuntu based virtual machine
images and standalone server installation packages.

The packages are available at:
http://chipster.sourceforge.net/downloads.shtml

Release notes are available at:
http://chipster.sourceforge.net/release_notes.shtml

You can update to Chipster 2.6.1 from within the virtual machine by using the
update.sh script. This script will simplify and speed up the update
process by only downloading and installing changed files. The script is
located in the /opt/chipster directory. Before running it you should
stop all the Chipster services.

The update.sh feature is still experimental, so backing things up before
running it is recommended.

Should you have any trouble, don't hesitate to drop a mail at
chi...@li...<mailto:chi...@li...> (or contact us directly, if you wish).

Cheers,

Taavi and the rest of the team


--
Taavi Hupponen, Chipster Team
CSC. P.O.Box 405, 02101 ESPOO, Finland
tel. +358-9-4572283 fax. +358-9-4572302
CSC - IT Center for Science, http://www.csc.fi<" rel="nofollow">http://www.csc.fi/>
email: taa...@cs...<mailto:taa...@cs...>

Hello all,

Chipster 2.5.1 has been released. It includes the mirna base bowtie indexes, which were missing in Chipster 2.5.0.

We are happy to announce that version 2.4 of Chipster server
environment is released as ready-to-run Ubuntu based virtual machine
images and standalone server installation packages.

The packages are available at:
http://chipster.sourceforge.net/downloads.shtml

Release notes are available at:
http://chipster.sourceforge.net/release_notes.shtml

If you are running Chipster virtual machine 2.0.2 or later, it is
possible to update to 2.5.1 from within the virtual machine by using the
update.sh script. This script will simplify and speed up the update
process by only downloading and installing changed files. The script is
located in the /opt/chipster directory. Before running it you should
stop all the Chipster services.

The update.sh feature is still experimental, so backing things up before
running it is recommended.

Should you have any trouble, don't hesitate to drop a mail at
chi...@li...<mailto:chi...@li...> (or contact us directly, if you wish).

Cheers,

Taavi and the rest of the team


--
Taavi Hupponen, Chipster Team
CSC. P.O.Box 405, 02101 ESPOO, Finland
tel. +358-9-4572283 fax. +358-9-4572302
CSC - IT Center for Science, http://www.csc.fi
email: taa...@cs...<mailto:taa...@cs...>

Hello all,

We are happy to announce that version 2.5 of Chipster server
environment is released as ready-to-run Ubuntu based virtual machine
images and standalone server installation packages.

The packages are available at:
http://chipster.sourceforge.net/downloads.shtml

Release notes are available at:
http://chipster.sourceforge.net/release_notes.shtml

If you are running Chipster virtual machine 2.0.2 or later, it is
possible to update to 2.5 from within the virtual machine by using the
update.sh script. This script will simplify and speed up the update
process by only downloading and installing changed files. The script is
located in the /opt/chipster directory. Before running it you should
stop all the Chipster services.

The update.sh feature is still experimental, so backing things up before
running it is recommended.

Should you have any trouble, don't hesitate to drop a mail at
chi...@li...<mailto:chi...@li...> (or contact us directly, if you wish).

Cheers,

Taavi and the rest of the team


--
Taavi Hupponen, Chipster Team
CSC. P.O.Box 405, 02101 ESPOO, Finland
tel. +358-9-4572283 fax. +358-9-4572302
CSC - IT Center for Science, http://www.csc.fi
email: taa...@cs...<mailto:taa...@cs...>

Hello all,

We are happy to announce that version 2.4 of Chipster server
environment is released as ready-to-run Ubuntu based virtual machine
images and standalone server installation packages.

The packages are available at:
http://chipster.sourceforge.net/downloads.shtml

Release notes are available at:
http://chipster.sourceforge.net/release_notes.shtml

If you are running Chipster virtual machine 2.0.2 or later, it is
possible to update to 2.4 from within the virtual machine by using the
update.sh script. This script will simplify and speed up the update
process by only downloading and installing changed files. The script is
located in the /opt/chipster directory. Before running it you should
stop all the Chipster services.

The update.sh feature is still experimental, so backing things up before
running it is recommended.

Should you have any trouble, don't hesitate to drop a mail at
chi...@li...<mailto:chi...@li...> (or contact us directly, if you wish).

Cheers,

Taavi and the rest of the team

Hello all,

We are happy to announce that version 2.3.0 of Chipster server
environment is released as ready-to-run Ubuntu based virtual machine
images and standalone server installation packages.

The packages are available at:
http://chipster.sourceforge.net/downloads.shtml

Release notes are available at:
http://chipster.sourceforge.net/release_notes.shtml

If you are running Chipster virtual machine 2.0.2 or later, it is
possible to update to 2.3.0 from within the virtual machine by using the
update.sh script. This script will simplify and speed up the update
process by only downloading and installing changed files. The script is
located in the /opt/chipster directory. Before running it you should
stop all the Chipster services.

The update.sh feature is still experimental, so backing things up before
running it is recommended.

Should you have any trouble, don't hesitate to drop a mail at
chi...@li...<mailto:chi...@li...> (or contact us directly, if you wish).

Cheers,

Taavi and the rest of the team

Hello all,

We are happy to announce that version 2.2.0 of Chipster server
environment is released as ready-to-run Ubuntu based virtual machine
images and standalone server installation packages.

The emphasis on this update is on new and improved NGS analysis tools.

The packages are available at:
http://chipster.sourceforge.net/downloads.shtml

Release notes are available at:
http://chipster.sourceforge.net/release_notes.shtml

If you are running Chipster virtual machine 2.0.2 or later, it is
possible to update to 2.2.0 from within the virtual machine by using the
update.sh script. This script will simplify and speed up the update
process by only downloading and installing changed files. The script is
located in the /opt/chipster directory. Before running it you should
stop all the Chipster services.

The update.sh feature is still experimental, so backing things up before
running it is recommended.

Should you have any trouble, don't hesitate to drop a mail at
chi...@li...<mailto:chi...@li...> (or contact us directly, if you wish).

Cheers,

Taavi and the rest of the team