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Michael P Schroeder
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Merge branch 'release-2.1.1'
Conflicts: changelog.md
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‎README.md‎

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@@ -9,13 +9,17 @@ Web site
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Documentation
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--------------
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+ See [Gitools documentation files](doc/source/index.rst) in the repository or at <http://help.gitools.org>
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+ See <http://help.gitools.org> or [Gitools documentation files](doc/source/index.rst) in the repository
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Source code
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-----------
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+ <https://github.com/gitools/gitools>
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Changelog
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----------
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+ see recent changes in the software in the [changelog](changelog.md)
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Versioning
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----------
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org.gitools.ui.app/src/main/resources/changelog.txt renamed to changelog.md

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Gitools 2.2.1
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-------------------------------------------------------------
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* New external commands: mutex-sort, close (and save)
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* Mutex bugfixes
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* Overlap wizard bugfixes
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* Exception bug fixes
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Gitools 2.2.0
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-------------------------------------------------------------
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* Mutual exclusion plugin (new)
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* New cancer genomics data .matibx compressed (new)
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* SVG image export (new)
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* Hierarchical cluster heatmap header with contextual menu (new)
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* View enrichment data via contextual menu in results (new)
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* Layer groups (new)
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* Recent files (new)
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* .mtabix data file compression (new)
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* Parellization: use multiple cores for many tasks
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* Many performance improvements
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* UI improvements
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* Correlation analysis
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* Enrichment analysis (binomial, z-score, fisher)
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* Overlapping analysis
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* Oncodrive analysis
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* Oncodrive analysis

‎doc/source/UserGuide_ExternalControl.rst‎

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Overview of commands
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-------------------------------------------------
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================================================ ============================================ ===================================================================================== ======================
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Command Description Options as of Version
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================================================ ============================================ ===================================================================================== ======================
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**add-header-colored-labels** Adds a new colored labels header 2.0.0
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- -c (--color) <color> : A Hex color as '#FF0000' - depends on --value
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- -h (--heatmap) <heatmap> : Heatmap name or ``last`` for the last added
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- -n (--no-auto-generate) : Specify if auto color generation is not desired.
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- -p (--pattern) <pattern> : The pattern of annotations as e.g. ${annotation-id}
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- -d (--dimension) <dim> : Indicate where to add the header: 'rows' or 'columns'.
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- -t (--text-visible) : Set for visible text labels
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- -v (--value) <value> : A value corresponding to a color
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================================================ ============================================ ========================================================================================= ======================
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Command Description Options as of Version
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================================================ ============================================ ========================================================================================= ======================
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**add-header-colored-labels** Adds a new colored labels header 2.0.0
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- ``-c (--color) <color>`` : A Hex color as '#FF0000' - depends on --value
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- ``-n (--no-auto-generate)`` : Specify if auto color generation is not desired.
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- ``-p (--pattern) <pattern>`` : The pattern of annotations as e.g. ${annotation-id}
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- ``-d (--dimension) <dim>`` : Indicate where to add the header: 'rows' or 'columns'.
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- ``-t (--text-visible)`` : Set for visible text labels
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- ``-v (--value) <value>`` : A value corresponding to a color
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- ``-h (--heatmap) <heatmap>`` : (Optional) Heatmap name or ``last`` for the last added
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**add-header-text-labels** Adds a new text header to the heatmap
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- -h (--heatmap) <heatmap> : Heatmap
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- -p (--pattern) <pattern> : The pattern of annotations as e.g. ${annotation-id} 2.0.0
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- -d (--dimension) <dim> : Indicate where to add the header: 'rows' or 'columns'.
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- ``-p (--pattern) <pattern>`` : The pattern of annotations as e.g. ${annotation-id} 2.0.0
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- ``-d (--dimension) <dim>`` : Indicate where to add the header: 'rows' or 'columns'.
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- ``-h (--heatmap) <heatmap>`` : Heatmap name. Not compulsory if one is open.
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**close** Closes a heatmap and optionally saves (as)
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- ``-a (--as) <FILE_NAME>`` : path and filename indicating where to save the heatmap 2.2.1
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- ``-d (--discard-hidden)`` : Discard hidden data
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- ``-h (--heatmap) <heatmap>`` : (optional) 'LAST' or heatmap name
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- ``-o (--optimize)`` : Optimize data file (slower saving process)
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- ``-s (--save)`` : Save current state as heatmap
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**help** Prints all available commands
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**load **\ matrix-file  Tells Gitools to load a file. - ``--rows** (-r)`` : File rows annotations 1.7.0
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- ``--cols (-c)`` : File cols annotations
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**sort-by-annotation** Sorts the heatmap by col or row annotation
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- -h (--heatmap) <heatmap> : Heatmap
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- -p (--pattern) <pattern> : The pattern of annotations as e.g. ${annotation-id} 2.2.0
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- -d (--dimension) <dim> : Indicate where to add the header: 'rows' or 'columns'.
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**load **\ matrix-file  Tells Gitools to load a file. - **--rows** ( **-r**) : File rows annotations 1.7.0
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- **--cols** ( **-c**) : File cols annotations
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**version** Prints Gitools version. 1.7.1
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================================================ ============================================ ===================================================================================== ======================
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- ``-p (--pattern) <pattern>`` : The pattern of annotations as e.g. ${annotation-id} 2.2.0
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- ``-d (--dimension) <dim>`` : Indicate where to add the header: 'rows' or 'columns'.
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- ``-h (--heatmap) <heatmap>`` : Heatmap name. Not compulsory if one is open.
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**sort-mutex** Sorts the visible layer by mutual excl.
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- ``-d (--dimension) <dimension>`` : Indicate where to add the header: 'rows' or 2.2.1
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'columns'.
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- ``-h (--heatmap) <heatmap>`` : (optional) 'LAST' or heatmap name
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- ``-i (--identifier) <identifier>`` : Specify this option for each identifier which
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you want to include in the mutex sorting
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- ``-p (--pattern) <pattern>`` : The pattern of annotations as e.g.
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${annotation-id}
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- ``-s (--sort) <sort>`` : Sort according to header. Specify either
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asc[ending] or desc[ending].
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**version** Prints Gitools version. 1.7.1
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================================================ ============================================ ========================================================================================= ======================
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.. code-block:: python
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import socket
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gitools = socket .socket(socket .AF\_INET, socket .SOCK\_STREAM)
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gitools .connect(( ’localhost’, 50151))
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command = ”load /home/user/matrix-file.tdm --cols /home/user/col-annotations.tsv --rows /home/user/row-annotations.tsv”
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gitools .send( command )
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gitools .close()
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def gitools_command(command):
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gitools = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
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gitools.connect(("localhost", 50151))
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gitools.sendall( command.encode('utf-8'))
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gitools.close()
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command = "load /home/user/matrix-file.tdm --cols /home/user/col-annotations.tsv --rows /home/user/row-annotations.tsv"
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gitools_command(command)

‎doc/source/conf.py‎

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# The short X.Y version.
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version = '2.2'
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# The full version, including alpha/beta/rc tags.
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release = '2.2.0'
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release = '2.2.1'
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# The language for content autogenerated by Sphinx. Refer to documentation
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# for a list of supported languages.

‎howto-release.txt‎

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git push
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# Start a new release or hotfix
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git-flow release start gitools-2.2.0
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git-flow hotfix start gitools-2.2.0
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git-flow release start gitools-2.2.1
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git-flow hotfix start gitools-2.2.1
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# Update pom.xml version
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# The following command only prints to display
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# Check that you are going to update only the correct versions:
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find . -name pom.xml | awk '{ system("sed 0,/2.1.0/s//2.2.0/ "$0)}' | grep -A2 -B3 2.2.0
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find . -name pom.xml | awk '{ system("sed 0,/2.1.0/s//2.2.1/ "$0)}' | grep -A2 -B3 2.2.1
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# The following command will apply the changes
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# Update all like this:
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find . -name pom.xml | awk '{ system("sed -i 0,/2.1.0/s//2.2.0/ "$0)}'
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find . -name pom.xml | awk '{ system("sed -i 0,/2.1.0/s//2.2.1/ "$0)}'
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# Go to Documentation folder.
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# Check in src/conf.py if the version numbers are up to date
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# Test new release
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unzip gitools-2.2.0-bin.zip
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gitools-2.2.0/bin/gitools
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unzip gitools-2.2.1-bin.zip
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gitools-2.2.1/bin/gitools
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# Deploy ZIP file
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scp target/gitools-2.2.0-bin.zip bgadmin@ankara:/usr/local/gitools/www/downloads/
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scp target/gitools-2.2.1-bin.zip bgadmin@ankara:/usr/local/gitools/www/downloads/
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# Deploy Webstart
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./webstart-deploy.sh 2.2.0
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./webstart-deploy.sh 2.2.1
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/usr/local/gitools/www/downloads/latest.txt
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# Commit the changes
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git commit -a -m "Release version 2.2.1"
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# Finish the release or hotfix
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git flow release finish gitools-2.2.0
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git flow hotfix finish gitools-2.2.0
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git flow release finish gitools-2.2.1
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git flow hotfix finish gitools-2.2.1
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# Check that you are on develop branch
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git checkout develop
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# Check that you are going to update only the correct versions:
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find . -name pom.xml | awk '{ system("sed 0,/2.2.0/s//2.2.0-SNAPSHOT/ "$0)}' | grep -A2 -B3 2.2.0-SNAPSHOT
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find . -name pom.xml | awk '{ system("sed 0,/2.2.1/s//2.3.0-SNAPSHOT/ "$0)}' | grep -A2 -B3 2.3.0-SNAPSHOT
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# Update all like this:
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find . -name pom.xml | awk '{ system("sed -i 0,/2.2.0/s//2.2.0-SNAPSHOT/ "$0)}'
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find . -name pom.xml | awk '{ system("sed -i 0,/2.2.1/s//2.3.0-SNAPSHOT/ "$0)}'
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# Commit
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git commit -a -m "Next iteration version 2.3.0-SNAPSHOT"
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git push origin
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‎lib/weblookandfeel/weblookandfeel/1.28-20140308/_maven.repositories‎

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‎lib/weblookandfeel/weblookandfeel/1.28-20140308/weblookandfeel-1.28-20140308.jar‎

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‎lib/weblookandfeel/weblookandfeel/1.28-20140308/weblookandfeel-1.28-20140308.jar.sha1‎

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‎lib/weblookandfeel/weblookandfeel/1.28-20140308/weblookandfeel-1.28-20140308.pom.md5‎

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