Page Comparison

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• R Installation
• Bioconductor
• Eclipse Plugin for R
  • Getting Started Guide for R Eclipse Plugin
• You'll also need to install some tools that R package builds depend upon:
  • Windows
    1. Download and unpack https://s3.amazonaws.com/nicole.deflaux/RStuff/DocumentationAndToolsForBuildingRPackageOnWindows.zip
    2. Follow the instructions on the first three slides of doc/buildingPackages110406.pdf for how to install all the tools
  • Mac OSX
    1. Install XCodeso that you have a C compiler
       • Be sure to select installation option "UNIX Development Support"
       • If you install from the "App Store" and are not presented with this option, the following is a work-around:

         • After installing Xcode, go to XCode>Preferences...

         • Go to Downloads > Command Line Tools > Install

         • Follow the prompts to register as an Apple Developer and download the tools.

    2. Install MacTex

Python

• Python Installation
• Python Introduction
• Python Unit Test Framework

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1. Make sure you are running the right version of easy_install http://superuser.com/questions/256717/easy-install-the-wrong-version-of-python-modules-mac-os

2. From the shell:

   Code Block

   ~/platform/trunk>easy_install progressbar Searching for progressbar Reading http://pypi.python.org/simple/progressbar/ Reading http://code.google.com/p/python-progressbar/ Reading http://code.google.com/p/python-progressbar Best match: progressbar 2.3 Downloading http://python-progressbar.googlecode.com/files/progressbar-2.3.tar.gz Processing progressbar-2.3.tar.gz Running progressbar-2.3/setup.py -q bdist_egg --dist-dir /var/folders/h0/h0pR5063FtCMCzzo1bt2WU+++TI/-Tmp-/easy_install-a29dGI/progressbar-2.3/egg-dist-tmp-3Dwzuw zip_safe flag not set; analyzing archive contents... Adding progressbar 2.3 to easy-install.pth file Installed /Library/Python/2.7/site-packages/progressbar-2.3-py2.7.egg Processing dependencies for progressbar Finished processing dependencies for progressbar

Python Examples for Perl programmers

1. Example: empty dictionary, add values to it

   Code Block
   layer = {} layer["type"] = row[1] layer["status"] = row[2] layer["name"] = row[3] layer["numSamples"] = row[4] layer["platform"] = row[5] layer["version"] = row[6] layer["qcBy"] = row[11]

2. Example: empty two level dictionary, add values to it

   Code Block
   layer = {} layer['foo'] = {} layer['foo']['bar'] = 3 layer['hello'] = {} layer['hello']['world'] = 42

3. Example: create a populated dictionary

   Code Block
   CSV_TO_PRIMARY_FIELDS = { 'name': 'name', 'description': 'description', 'Investigator': 'creator', 'Creation Date': 'creationDate', 'Status': 'status', 'date_released': 'releaseDate', 'version':'version' }

4. Example: create a populated two-level dictionary

   Code Block
   MY_FAKE_LAYER = {'foo': {'bar': 3}, 'hello': {'world': 42}}

5. Example: empty array, add values to it

   Code Block
   stringAnnotations = [] stringAnnotations.append("foo")

6. Example: create a populated array

   Code Block
   CSV_SKIP_FIELDS = ["db_id","user_agreement_file_path", "readme_file_path"];

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How to Set Up Merge Tracking

1. Download svnmerge.py

2. Make a branch directory for yourself (you'll only need to do this once)

   Code Block
   svn mkdir https://sagebionetworks.jira.com/svn/PLFM/branches/deflaux

3. Make a new branch from trunk

   Code Block
   svn copy https://sagebionetworks.jira.com/svn/PLFM/trunk https://sagebionetworks.jira.com/svn/PLFM/branches/deflaux/automatedIntegrationTesting

4. Have both trunk and your new branch on your local hard drive, this assumes you already have trunk checked out in directory ~/platform

   Code Block
   cd ~/platform svn update trunk svn checkout https://sagebionetworks.jira.com/svn/PLFM/branches/deflaux/automatedIntegrationTesting

5. Initialize merge tracking

   Code Block
   cd trunk svnmerge.py init ../automatedIntegrationTesting svn commit -F svnmerge-commit-message.txt cd ../automatedIntegrationTesting svnmerge.py init ../trunk svn commit -F svnmerge-commit-message.txt

Alternative: Initialize merge tracking and switch to your new branch

cd trunk
svnmerge.py init https://sagebionetworks.jira.com/svn/PLFM/branches/deflaux/sts
svn commit -F svnmerge-commit-message.txt
svn switch https://sagebionetworks.jira.com/svn/PLFM/branches/deflaux/sts
svnmerge.py init https://sagebionetworks.jira.com/svn/PLFM/trunk
svn commit -F svnmerge-commit-message.txt

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1. Ensure the branch is working and committed to SVN.

2. To see what changes and/or branches are available for importing, use this command from the branch distribution:

   Code Block
   python svnmerge.py avail -l

   • Windows Users: One of the results should be '/PLFM/trunk'.
3. import the changes from trunk into the branch:

   • to merge all changes

     Code Block
     python svnmerge.py merge -S /PLFM/trunk

   • to merge one or more particular changes

     Code Block
     python svnmerge.py merge -r #,#,# -S /PLFM/trunk

4. Resolve conflicts, compile, test and commit EVERYTHING in the branch.

   Code Block
   svn ci -F svnmerge-commit-message.txt

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1. Go to an up-to-date local distribution of trunk.
2. From the trunk distribution use the 'avail' command (above) to find the branch of interest.

3. Use the following command to find the revision(s) of interest:

   Code Block
   python svnmerge.py avail -S <your branch>

4. Import the changes from the branch into trunk:

   1. For all changes

      Code Block
      python svnmerge.py merge -S <your branch>

   2. For particular changes

      Code Block
      python svnmerge.py merge -r <your revisions comma separated> -S <your branch>

5. Resolve conflicts, compile, test and commit.

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