Bklein7 Week 12

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Genome Sequencing Paper PowerPoint Presentation

Presentation File (PDF): File:Genomepaper cw20151116.pdf

Quality Assurance Work

I created and tested our first Bordetella pertussis gene database, tagged cw20151119.

Work Log:

  • Thursday, November 19: I followed the import-export process for the creation of our first Bordetella pertussis gene database. My protocol was documented on the Gene Database Testing Report page for this database.
  • Monday, November 23: I accessed the exported database and went through counting protocols to evaluate its content. Results were posted on the Gene Database Testing Report page for this database.

Coder Work

Before proceeding, I designated my personal laptop as my development computer.

GitHub Repository Clone Setup

GitHub Information:

GitHub Clone Setup:

  1. I designated a folder on my Desktop entitled "B. pertussis Project" as the location for my local copy of the XMLPipeDB GitHub repository. To enter this location, I opened Terminal and used the following command: 
    cd /Users/brandonklein/Desktop/B.\ pertussis\ Project
  2. I cloned the repository:
    git clone https://github.com/lmu-bioinformatics/xmlpipedb.git
  3. I entered the clone folder: 
    cd xmlpipedb
  4. I switched to my branch:
    git checkout b-pertussis

“Developer Rig” Setup and Initial As-Is Build

Necessary software was downloaded:

  • Java developer tools: JDK 8 (which, at this writing, is JDK 8u65)
  • Any tool that can unpack .gz and .zip files: Keka (listed as an equivalent software to 7-zip for Mac OS X)
  • XMLPipeDB Match utility
  • Development environment: Eclipse IDE for Java EE Developers

Eclipse Workspace Setup

  1. I ran Eclipse.
  2. When prompted to specify a Workspace, I selected my "xmlpipedb" repository clone folder and clicked "Open".
  3. I verified that my repository clone folder was listed as the Workspace: and clicked OK.
  4. When presented with the introductory display, I clicked the Workbench button.
    • This took me to an empty developer area:
    • Screen Shot 2015-11-23 at 5.10.28 PM.png

Java Project Setup

  1. I right-clicked within the empty Project Explorer tab and chose New > Project… from the menu that appeared.
  2. I chose Java Project from the list of “wizards” and clicked on the Next > button.
  3. On the next panel, I entered gmbuilder as the Project name:.
    • The JRE section showed Java 1.8, confirming that my version of Java was up to date.
  4. I click on the Finish button.
    • When asked if I wanted to open the “Java perspective,” I responded with Yes.
  5. The gmbuilder project folder was now visible in the Project Explorer tab.
    • The gmbuilder project folder did not show a red x icon.

Initial Build

  1. I opened the gmbuilder project by clicking on the gray triangle to the left of its name.
  2. I right-clicked on build.xml listing and chose Run As > Ant Build... from the menu that appears.
  3. In the Edit Configuration dialog that appears, I entered the "Targets" tab. There, I checked on the clean and dist items in the Targets tab. The Target execution order section near the bottom of the dialog displayed clean, dist.
  4. I clicked the Run button. After 3 seconds of processing, the build was successful.
  5. When this was done, I right-clicked on the gmbuilder project folder and chose Refresh from the menu that appears.
  6. A dist folder was now present inside the gmbuilder project folder. This was my personally-built copy of GenMAPP Builder. Its contents correspond to the extracted contents of the gmbuilder-3.0.0-build-5.zip file that was downloaded in class.
    • Screenshot of my copy of gmbuilder within the Eclipse working environment:
    • Eclipse gmbuilder Ant Build.png

Links

Assignments Pages

Individual Journal Entries

Shared Journal Entries

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