Kayako 13271

API_UG.yml

@@ -16,6 +16,7 @@ pages:
   - BAM Slicing: 'API/Users_Guide/BAM_Slicing.md'
   - Submission: 'API/Users_Guide/Submission.md'
   - Python Examples: 'API/Users_Guide/Python_Examples.md'
+  - GraphQL Examples: 'API/Users_Guide/GraphQL_Examples.md'
   - System Information: 'API/Users_Guide/System_Information.md'
   - Additional Examples: 'API/Users_Guide/Additional_Examples.md'
   - "Appendix A: Available Fields": 'API/Users_Guide/Appendix_A_Available_Fields.md'

Data_Submission_Portal_UG.yml

@@ -9,19 +9,13 @@ copyright: "© 2015-2016"
 theme_dir: theme
 pages:
 - Data Submission Portal:
-  - Getting Started: 'Data_Submission_Portal/Users_Guide/Getting_Started.md'
-  - Submission Workflow: 'Data_Submission_Portal/Users_Guide/Submission_Workflow.md'
-  - Authentication: 'Data_Submission_Portal/Users_Guide/Authentication.md'
-  - Homepage: 'Data_Submission_Portal/Users_Guide/Homepage.md'
-  - Dashboard: 'Data_Submission_Portal/Users_Guide/Dashboard.md'
-  - Upload Data: 'Data_Submission_Portal/Users_Guide/Data_Upload_UG.md'
-  - Submit Data: 'Data_Submission_Portal/Users_Guide/Submit_Data.md'
-  - Release Data: 'Data_Submission_Portal/Users_Guide/Release_Data.md'
-  - Transactions: 'Data_Submission_Portal/Users_Guide/Transactions.md'
-  - Browse Data: 'Data_Submission_Portal/Users_Guide/Browse_Data.md'
-  - Pre-Release Data Review: 'Data_Submission_Portal/Users_Guide/Pre_Release_QC.md'
-  - Best Practices: 'Data_Submission_Portal/Users_Guide/Best_Practices.md'
+  - Before Submitting Data to the GDC Portal: 'Data_Submission_Portal/Users_Guide/Checklist.md'
+  - Data Submission Overview: 'Data_Submission_Portal/Users_Guide/Data_Submission_Overview.md'
+  - Data Submission Portal: 'Data_Submission_Portal/Users_Guide/Data_Submission_Process.md'
+  - Data Upload Walkthrough: 'Data_Submission_Portal/Users_Guide/Data_Submission_Walkthrough.md'
+  - Pre-Release Data Portal: 'Data_Submission_Portal/Users_Guide/Pre_Release_QC.md'
   - Release Notes: 'Data_Submission_Portal/Release_Notes/Data_Submission_Portal_Release_Notes.md'
+
 extra:
   project_root_dir: '/'
   project_org: 'GDC'

Data_Transfer_Tool_UG.yml

@@ -10,12 +10,10 @@ theme_dir: theme
 pages:
 - Data Transfer Tool:
   - Getting Started: 'Data_Transfer_Tool/Users_Guide/Getting_Started.md'
-  - Accessing Built-in Help: 'Data_Transfer_Tool/Users_Guide/Accessing_Built-in_Help.md'
   - Preparing for Data Download and Upload: 'Data_Transfer_Tool/Users_Guide/Preparing_for_Data_Download_and_Upload.md'
-  - Data Download and Upload - Command Line: 'Data_Transfer_Tool/Users_Guide/Data_Download_and_Upload.md'
-  - Data Download - UI: 'Data_Transfer_Tool/Users_Guide/Data_Download_Upload_UI.md'
-  - Key Terms: 'Data_Transfer_Tool/Users_Guide/Appendix_A_-_Key_Terms.md'
+  - Data Transfer Tool Command Line Documentation: 'Data_Transfer_Tool/Users_Guide/Data_Download_and_Upload.md'
   - Release Notes - Command Line: 'Data_Transfer_Tool/Release_Notes/DTT_Release_Notes.md'
+  - Data Transfer Tool UI Documentation: 'Data_Transfer_Tool/Users_Guide/Data_Download_DTT_UI.md'
   - Release Notes - UI: 'Data_Transfer_Tool/Release_Notes/DTT_UI_Release_Notes.md'
 
 extra:

Data_UG.yml

@@ -19,6 +19,7 @@ pages:
   - "Bioinformatics Pipeline: miRNA Analysis": 'Data/Bioinformatics_Pipelines/miRNA_Pipeline.md'
   - "Bioinformatics Pipeline: Copy Number Variation": 'Data/Bioinformatics_Pipelines/CNV_Pipeline.md'
   - "Bioinformatics Pipeline: Methylation Liftover": 'Data/Bioinformatics_Pipelines/Methylation_LO_Pipeline.md'
+  - Aligned Reads Summary Metrics: 'Data/Bioinformatics_Pipelines/Aligned_reads_summary_metrics.md'
   - Release Notes: 'Data/Release_Notes/Data_Release_Notes.md'
 extra:
   project_root_dir: '/'

README.md

@@ -1,7 +1,97 @@
 ![](https://gdc.cancer.gov/sites/all/themes/gdc_bootstrap/logo.png)
 
-# THIS PROJECT HAS MOVED
+# GDC Open Source code
 
-Please join us at https://github.com/NCI-GDC/gdc-docs
+=======
+GDC is Open Source, Github Repositories containing source code of GDC Applications can be found on [GDC GitHub Organization page](https://github.com/NCI-GDC/).
 
+- GDC Data Portal: https://github.com/NCI-GDC/portal-ui
+- GDC Legacy Archive: https://github.com/NCI-GDC/portal-ui-legacy
+- GDC Data Transfer Tool: https://github.com/NCI-GDC/gdc-client
+- GDC Data Dictionary: https://github.com/NCI-GDC/gdcdictionary
+- GDC Data Model: https://github.com/NCI-GDC/gdcdatamodel
+- GDC Psqlgraph: https://github.com/NCI-GDC/psqlgraph 
+
+# Support
+
+Please direct technical questions to [GDC Support](https://gdc.cancer.gov/support).
+
+# GDC Documentation Site
+
+### Technology
+
+ - Python 2.6, 2.7, 3.3, 3.4 and 3.5.
+ - [mkdocs](http://www.mkdocs.org/)
+ - [BSCodeTabs for mkdocs](https://github.com/mikecules/MarkdownBSCodeTabs#for-use-in-mkdocs)
+
+### Install & Run
+
+(Optional) Set up virtualenv:
+
+- [Install virtualenv](https://packaging.python.org/guides/installing-using-pip-and-virtual-environments/)
+- `python -m virtualenv venv`
+- `source venv/bin/activate`
+- Run the installation commands below
+- To leave the virtual environment: `deactivate`
+
+Install GDC-docs:
+
+ - `pip install -r requirements.txt`
+ - `mkdocs serve` (optionally set port `--dev-addr=0.0.0.0:<PORT>`)
+
+### Build
+
+ - `mkdocs build --clean`
+
+### Repository Conventions
+
+- All Shared content in the "Commons" directory
+- One Directory per GDC product (API, Data_Portal, Data_Submission_Portal, Data_Transfer_Tool)
+- Each GDC product have a Users_Guide and Release_Notes directory
+
+### Linking
+
+To another documentation page
+```
+[Authentication and Authorization](../../Commons/Authentication.md)
+```
+
+Inside another documentation page
+
+```
+[Authentication and Authorization](../../Commons/Authentication.md#internal-section)
+```
+
+### Adding icons and PDFs
+The convention for this, when updating mkdocs.yml is the following:
+- <font-awesome-icon> <content> <url ending in .pdf>: 'index.md'
+example:
+- fa-file-pdf-o Download PDF /API/PDF/API_UG.pdf: 'index.md'
+
+### Documentation Conventions
+
+A detailed list of all conventions is available on [GDC Website](https://gdc.cancer.gov/conventions-page)
+
+
+### Build PDF
+
+Install mkdocs2pandoc, following instructions available here:
+```
+https://github.com/jgrassler/mkdocs-pandoc
+```
+
+Prepare a yml file dedicated to your Userguide, using Data_Portal_UG.yml as an example.
+
+Run the following commands to:
+* Convert the User Guide to Pandoc:
+* Tweak the pandoc file
+* Build a PDF
+
+```
+mkdocs2pandoc -f Data_Portal_UG.yml -o docs/Data_Portal/PDF/Data_portal_UG.pd
+sed -i -e 's/# / /g' docs/Data_Portal/PDF/Data_portal_UG.pd
+sed -i -e 's/### /## /g' docs/Data_Portal/PDF/Data_portal_UG.pd
+sed -i -e 's/\/site\//\/docs\//g' docs/Data_Portal/PDF/Data_portal_UG.pd
+pandoc --toc -V documentclass=report -V geometry:"top=2cm, bottom=1.5cm, left=1cm, right=1cm" -f markdown+grid_tables+table_captions -o docs/Data_Portal/PDF/Data_portal_UG.pdf docs/Data_Portal/PDF/Data_portal_UG.pd
+```