Recent changes to TechnicalManual20

TechnicalManual20 modified by Aleksi Kallio

Aleksi Kallio — Fri, 11 Jul 2014 12:32:09 -0000

--- v74
+++ v75
@@ -1,6 +1,7 @@
-[TOC]
-
 # Technical manual for Chipster 2.0
+
+> **Note! This is an unmaintained archive site.**
+> Wiki has been moved to Github and current documentation is available at [https://github.com/chipster/chipster/wiki](https://github.com/chipster/chipster/wiki)

 The manual covers Chipster platform version 2.0. It instructs in setting up your own Chipster server, adding your own tools into Chipster, and more. For the user manual, please see http://chipster.csc.fi/manual/.

TechnicalManual20 modified by Aleksi Kallio

Aleksi Kallio — Thu, 26 Jun 2014 06:42:31 -0000

--- v73
+++ v74
@@ -633,7 +633,7 @@

 ### Writing SADL header

-SADL (Simple Analysis Description Language) is a simple notation for describing analysis tools so that they can be used in the Chipster 2.0 framework. SADL describes what input files the tool takes, what output files it produces, and what parameters are needed for running it. For the syntax of SADL please see [SADLFormat] 
+SADL (Simple Analysis Description Language) is a simple notation for describing analysis tools so that they can be used in the Chipster 2 framework. SADL describes what input files the tool takes, what output files it produces, and what parameters are needed for running it. For the syntax of SADL please see [SADLFormat] 

 ### Making R scripts Chipster compatible

@@ -660,7 +660,7 @@
   * The default data format is TSV (tab separated values), with one row for each gene or probeset 
   * The first column should be unnamed or "identifier" and contain the gene/probeset name 
   * Tool should not remove any existing columns unless the row structure is changed. In other words, inputs can have annotation etc. data that just passes through analysis steps 
-  * See AnalysisToolInputsAndOutputs for more information, in version 2.0 typing will be decided by the analysis module and will be described in this page 
+  * See AnalysisToolInputsAndOutputs for more information 

 ### Sequence analysis module (Embster)

TechnicalManual20 modified by Aleksi Kallio

Aleksi Kallio — Thu, 26 Jun 2014 06:42:31 -0000

--- v72
+++ v73
@@ -331,7 +331,7 @@

 The system works so that the update.sh script is just a bootstrap script that downloads the actual update script and executes it. This way the update system itself also gets updated when needed. 

-The actual update script is called update-exec.sh and is located at [[http://www.nic.funet.fi/pub/sci/molbi.../updates/](http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/|http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/)]. When run, update-exec.sh downloads files, unpacks them, moves things around when needed and does other required setup steps. 
+The actual update script is called update-exec.sh and is located at <http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/>. When run, update-exec.sh downloads files, unpacks them, moves things around when needed and does other required setup steps. 

 Chipster update system only concerns the Chipster installation and tool dependencies. You should also take care of keeping the operating system of the VM installation up to date, using normal Debian tools, such as aptitude. 

@@ -353,7 +353,7 @@
   * chipster/comp/modules - custom tool scripts 
   * chipster/webstart/web-root/manual - custom manual pages 

-When Chipster is upgraded, also tool dependencies need updating. For exact details on changes between versions, look at the update-exec.sh script at [http://www.nic.funet.fi/pub/sci/molbi.../updates/](http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/|http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/). 
+When Chipster is upgraded, also tool dependencies need updating. For exact details on changes between versions, look at the update-exec.sh script at <http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/>. 

 ## Directory layout

TechnicalManual20 modified by Aleksi Kallio

Aleksi Kallio — Thu, 26 Jun 2014 06:42:30 -0000

--- v71
+++ v72
@@ -331,7 +331,7 @@

 The system works so that the update.sh script is just a bootstrap script that downloads the actual update script and executes it. This way the update system itself also gets updated when needed. 

-The actual update script is called update-exec.sh and is located at [http://www.nic.funet.fi/pub/sci/molbi.../updates/](http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/|http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/). When run, update-exec.sh downloads files, unpacks them, moves things around when needed and does other required setup steps. 
+The actual update script is called update-exec.sh and is located at [[http://www.nic.funet.fi/pub/sci/molbi.../updates/](http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/|http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/)]. When run, update-exec.sh downloads files, unpacks them, moves things around when needed and does other required setup steps. 

 Chipster update system only concerns the Chipster installation and tool dependencies. You should also take care of keeping the operating system of the VM installation up to date, using normal Debian tools, such as aptitude.

TechnicalManual20 modified by Aleksi Kallio

Aleksi Kallio — Thu, 26 Jun 2014 06:42:30 -0000

--- v70
+++ v71
@@ -331,7 +331,7 @@

 The system works so that the update.sh script is just a bootstrap script that downloads the actual update script and executes it. This way the update system itself also gets updated when needed. 

-The actual update script is called update-exec.sh and is located at [http://www.nic.funet.fi/pub/sci/molbi.../updates/](http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/). When run, update-exec.sh downloads files, unpacks them, moves things around when needed and does other required setup steps. 
+The actual update script is called update-exec.sh and is located at [http://www.nic.funet.fi/pub/sci/molbi.../updates/](http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/|http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/). When run, update-exec.sh downloads files, unpacks them, moves things around when needed and does other required setup steps. 

 Chipster update system only concerns the Chipster installation and tool dependencies. You should also take care of keeping the operating system of the VM installation up to date, using normal Debian tools, such as aptitude. 

@@ -353,7 +353,7 @@
   * chipster/comp/modules - custom tool scripts 
   * chipster/webstart/web-root/manual - custom manual pages 

-When Chipster is upgraded, also tool dependencies need updating. For exact details on changes between versions, look at the update-exec.sh script at [http://www.nic.funet.fi/pub/sci/molbi.../updates/](http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/). 
+When Chipster is upgraded, also tool dependencies need updating. For exact details on changes between versions, look at the update-exec.sh script at [http://www.nic.funet.fi/pub/sci/molbi.../updates/](http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/|http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/). 

 ## Directory layout

TechnicalManual20 modified by Aleksi Kallio

Aleksi Kallio — Thu, 26 Jun 2014 06:42:30 -0000

--- v69
+++ v70
@@ -322,17 +322,22 @@
 ### Upgrading VM bundled installation

 Since version 2.0.2, Chipster VM bundle comes with automatic update tool that allows you to update the installation without downloading everything again. Updates do not happen automatically, but must be initiated manually. Before the update, you should stop Chipster server. 
-
-./chipster stop ./update.sh ./chipster start 
-
-  
+    
+    
+    ./chipster stop
+    ./update.sh
+    ./chipster start
+    
+
 The system works so that the update.sh script is just a bootstrap script that downloads the actual update script and executes it. This way the update system itself also gets updated when needed. 

 The actual update script is called update-exec.sh and is located at [http://www.nic.funet.fi/pub/sci/molbi.../updates/](http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/). When run, update-exec.sh downloads files, unpacks them, moves things around when needed and does other required setup steps. 

 Chipster update system only concerns the Chipster installation and tool dependencies. You should also take care of keeping the operating system of the VM installation up to date, using normal Debian tools, such as aptitude. 
-
-sudo aptitude upgrade 
+    
+    
+    sudo aptitude upgrade
+    

 Operating system packages get updated and a reboot might be necessary.

TechnicalManual20 modified by Aleksi Kallio

Aleksi Kallio — Thu, 26 Jun 2014 06:42:29 -0000

--- v68
+++ v69
@@ -319,16 +319,36 @@

 ## Upgrading server installation

-Chipster 2.0 is a new major version and should be installed from scratch. 
-
-  
-
-
-  
-
-
-  
-
+### Upgrading VM bundled installation
+
+Since version 2.0.2, Chipster VM bundle comes with automatic update tool that allows you to update the installation without downloading everything again. Updates do not happen automatically, but must be initiated manually. Before the update, you should stop Chipster server. 
+
+./chipster stop ./update.sh ./chipster start 
+
+  
+The system works so that the update.sh script is just a bootstrap script that downloads the actual update script and executes it. This way the update system itself also gets updated when needed. 
+
+The actual update script is called update-exec.sh and is located at [http://www.nic.funet.fi/pub/sci/molbi.../updates/](http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/). When run, update-exec.sh downloads files, unpacks them, moves things around when needed and does other required setup steps. 
+
+Chipster update system only concerns the Chipster installation and tool dependencies. You should also take care of keeping the operating system of the VM installation up to date, using normal Debian tools, such as aptitude. 
+
+sudo aptitude upgrade 
+
+Operating system packages get updated and a reboot might be necessary. 
+
+  
+
+
+### Upgrading other installations
+
+If you installed Chipster yourself, then the automatic update mechanism is not available. The recommended approach is to make a fresh install of Chipster and move relevant functionality over from the previous installation. You should check at least these locations for things to move over: 
+
+  * chipster/*/conf/chipster-config.xml - custom configuration 
+  * chipster/comp/conf/runtimes.xml - custom analysis tool runtimes 
+  * chipster/comp/modules - custom tool scripts 
+  * chipster/webstart/web-root/manual - custom manual pages 
+
+When Chipster is upgraded, also tool dependencies need updating. For exact details on changes between versions, look at the update-exec.sh script at [http://www.nic.funet.fi/pub/sci/molbi.../updates/](http://www.nic.funet.fi/pub/sci/molbio/chipster/dist/virtual_machines/updates/). 

 ## Directory layout

TechnicalManual20 modified by Aleksi Kallio

Aleksi Kallio — Thu, 26 Jun 2014 06:42:29 -0000

--- v67
+++ v68
@@ -13,6 +13,8 @@
 # System installation

 ## Virtual machine installation
+
+The recommended way to get Chipster server running is virtual machine installation. Chipster is packaged as complete virtual machine images that can be deployed to a variety of virtualisation platforms. The images are based on Ubuntu Linux 11.10 (Oneiric). 

 ** To use the Chipster virtual machine, you need to:**

TechnicalManual20 modified by Aleksi Kallio

Aleksi Kallio — Thu, 26 Jun 2014 06:42:28 -0000

--- v66
+++ v67
@@ -57,7 +57,7 @@
 #### Start Chipster virtual machine

   * Select "Start" 
-    * _Note: In Mac environment, the presence of VMware tools in the image sometimes cause troubles during the boot (stops with kernel panic). These are solved by a reboot. In future versions of the virtual machines VMware tools will disabled by default._
+    * _Note: In Mac environment, the presence of VMware tools in the image sometimes causes troubles during the boot (freezes with kernel panic). It is solved by a reboot. In future versions of the virtual machine VMware tools will disabled by default._

 ### Instructions for VMware Player

TechnicalManual20 modified by Aleksi Kallio

Aleksi Kallio — Thu, 26 Jun 2014 06:42:28 -0000

--- v65
+++ v66
@@ -57,9 +57,7 @@
 #### Start Chipster virtual machine

   * Select "Start" 
-
-  
-
+    * _Note: In Mac environment, the presence of VMware tools in the image sometimes cause troubles during the boot (stops with kernel panic). These are solved by a reboot. In future versions of the virtual machines VMware tools will disabled by default._

 ### Instructions for VMware Player