Syncronized Pipeline Docs Directory Structure.

RenneLab · Feb 29, 2020 · 81353b6 · 81353b6
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Showing 16 changed files with 25 additions and 25 deletions.
diff --git a/docs/sample_01_link.rst b/docs/sample_01_link.rst
@@ -0,0 +1,2 @@
+
+.. include:: ../sample_01_summary_analysis/summary_analysis_notes.rst
diff --git a/docs/sample_02_link.rst b/docs/sample_02_link.rst
@@ -0,0 +1,2 @@
+
+.. include:: ../sample_02_target_analysis/target_analysis_notes.rst
diff --git a/docs/sample_03_link.rst b/docs/sample_03_link.rst
@@ -0,0 +1,2 @@
+
+.. include:: ../sample_03_grouped_target_analysis/grouped_target_analysis_notes.rst
diff --git a/docs/sample_04_link.rst b/docs/sample_04_link.rst
@@ -0,0 +1,2 @@
+
+.. include:: ../sample_04_fold_analysis/fold_analysis_notes.rst
diff --git a/docs/sample_05_link.rst b/docs/sample_05_link.rst
@@ -0,0 +1,2 @@
+
+.. include:: ../sample_05_fold_target_region_analysis/fold_target_region_notes.rst
diff --git a/docs/source/example_pipelines.rst b/docs/source/example_pipelines.rst
@@ -5,9 +5,9 @@ Example Pipelines
 .. toctree::
    :maxdepth: 4
 
-   sample_01_link
-   sample_02_link
-   sample_03_link
-   sample_04_link
-   sample_05_link
+   /sample_01_link
+   /sample_02_link
+   /sample_03_link
+   /sample_04_link
+   /sample_05_link
 
diff --git a/docs/source/sample_01_link.rst b/docs/source/sample_01_link.rst
diff --git a/docs/source/sample_02_link.rst b/docs/source/sample_02_link.rst
diff --git a/docs/source/sample_03_link.rst b/docs/source/sample_03_link.rst
diff --git a/docs/source/sample_04_link.rst b/docs/source/sample_04_link.rst
diff --git a/docs/source/sample_05_link.rst b/docs/source/sample_05_link.rst
diff --git a/sample_01_summary_analysis/summary_analysis_notes.rst b/sample_01_summary_analysis/summary_analysis_notes.rst
@@ -25,8 +25,8 @@ The completed output of the analysis requires ~1.5 Gb of space.
 Summary Analysis Example Output
 -------------------------------
 
-.. image:: /../sample_01_summary_analysis/example_output/combined_analysis_types_hybrids.png
+.. image:: ../sample_01_summary_analysis/example_output/combined_analysis_types_hybrids.png
 
-.. image:: /../sample_01_summary_analysis/example_output/combined_analysis_types_seg.png
+.. image:: ../sample_01_summary_analysis/example_output/combined_analysis_types_seg.png
 
-.. image:: /../sample_01_summary_analysis/example_output/combined_analysis_mirna_count.png
+.. image:: ../sample_01_summary_analysis/example_output/combined_analysis_mirna_count.png
diff --git a/sample_02_target_analysis/target_analysis_notes.rst b/sample_02_target_analysis/target_analysis_notes.rst
@@ -31,6 +31,6 @@ The completed output of the analysis requires ~20 Mb of space.
 Target Analysis Example Output
 ------------------------------
 
-.. image:: /../sample_02_target_analysis/example_output/GSM2720020_WT_BR1_KSHV_only_kshv-miR-K12-5.png
+.. image:: ../sample_02_target_analysis/example_output/GSM2720020_WT_BR1_KSHV_only_kshv-miR-K12-5.png
 
-.. image:: /../sample_02_target_analysis/example_output/GSM2720020_WT_BR1_KSHV_only_kshv-miR-K12-5_types.png
+.. image:: ../sample_02_target_analysis/example_output/GSM2720020_WT_BR1_KSHV_only_kshv-miR-K12-5_types.png
diff --git a/sample_03_grouped_target_analysis/grouped_target_analysis_notes.rst b/sample_03_grouped_target_analysis/grouped_target_analysis_notes.rst
@@ -33,6 +33,6 @@ The completed output of the analysis requires ~40 Mb of space.
 Grouped Target Analysis Example Output
 --------------------------------------
 
-.. image:: /../sample_03_grouped_target_analysis/example_output/KSHV_Hyb_Combined_kshv-miR-K12-1star.png
+.. image:: ../sample_03_grouped_target_analysis/example_output/KSHV_Hyb_Combined_kshv-miR-K12-1star.png
 
-.. image:: /../sample_03_grouped_target_analysis/example_output/KSHV_Hyb_Combined_kshv-miR-K12-1star_types.png
+.. image:: ../sample_03_grouped_target_analysis/example_output/KSHV_Hyb_Combined_kshv-miR-K12-1star_types.png
diff --git a/sample_04_fold_analysis/fold_analysis_notes.rst b/sample_04_fold_analysis/fold_analysis_notes.rst
@@ -36,5 +36,5 @@ The completed output of the analysis requires ~30 Mb of space.
 Fold Analysis Example Output
 --------------------------------------
 
-.. image:: /../sample_04_fold_analysis/example_output/WT_BR1_comp_hOH7_KSHV_hybrids_ua_coding.png
+.. image:: ../sample_04_fold_analysis/example_output/WT_BR1_comp_hOH7_KSHV_hybrids_ua_coding.png
 
diff --git a/sample_05_fold_target_region_analysis/fold_target_region_notes.rst b/sample_05_fold_target_region_analysis/fold_target_region_notes.rst
@@ -40,6 +40,6 @@ The completed output of the analysis requires ~50 Mb of space.
 Fold Target Region Analysis Example Output
 ------------------------------------------
 
-.. image:: /../sample_05_fold_target_region_analysis/example_output/WT_BR1_comp_hOH7_KSHV_kshv_3pUTR.png
+.. image:: ../sample_05_fold_target_region_analysis/example_output/WT_BR1_comp_hOH7_KSHV_kshv_3pUTR.png
 
-.. image:: /../sample_05_fold_target_region_analysis/example_output/WT_BR1_comp_hOH7_KSHV_cellular_3pUTR.png
+.. image:: ../sample_05_fold_target_region_analysis/example_output/WT_BR1_comp_hOH7_KSHV_cellular_3pUTR.png