From 7e123b73164d4c1df387d598b3843ddc169d6e24 Mon Sep 17 00:00:00 2001
From: "Vera Alvarez, Roberto" <veraalva@ncbi.nlm.nih.gov>
Date: Thu, 8 Jul 2021 12:31:36 -0400
Subject: [PATCH] Adding transcriptome annotation pipeline

---
 docs/source/index.rst                          |  1 +
 .../transcriptomeAnnotationPipeline.rst        | 12 ++++++++++++
 setup.py                                       |  4 +++-
 src/pm4ngs/main.py                             | 18 ++++++++++++++++++
 4 files changed, 34 insertions(+), 1 deletion(-)
 create mode 100644 docs/source/pipelines/transcriptomeAnnotationPipeline.rst

diff --git a/docs/source/index.rst b/docs/source/index.rst
index 0fdd742..56de45d 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -32,6 +32,7 @@ PM4NGS
    pipelines/rnaseqDGAPipeline
    pipelines/chipseqPipeline
    pipelines/chipexoPipeline
+   pipelines/transcriptomeAnnotationPipeline
    pipelines/creatingNewPipeline
    pipelines/utils
    pipelines/genomes
diff --git a/docs/source/pipelines/transcriptomeAnnotationPipeline.rst b/docs/source/pipelines/transcriptomeAnnotationPipeline.rst
new file mode 100644
index 0000000..139876d
--- /dev/null
+++ b/docs/source/pipelines/transcriptomeAnnotationPipeline.rst
@@ -0,0 +1,12 @@
+.. _transcriptomeAnnotationPipeline:
+
+#########################################################
+Transcriptome Annotation pipeline for non-model organisms
+#########################################################
+
+.. ATTENTION::
+
+    This annotation pipeline uses Google Cloud platform for all computing demand tasks. Users should have installed
+    and configured `Cloud SDK`_.
+
+.. _Cloud SDK: https://cloud.google.com/sdk/docs/quickstart
diff --git a/setup.py b/setup.py
index a7c02c5..0a148b3 100644
--- a/setup.py
+++ b/setup.py
@@ -78,7 +78,9 @@ def readme():
             'pm4ngs-chipseq = pm4ngs.main:chipseq',
             'pm4ngs-chipseq-demo = pm4ngs.main:chipseq_demo',
             'pm4ngs-chipexo = pm4ngs.main:chipexo',
-            'pm4ngs-chipexo-demo = pm4ngs.main:chipexo_demo'
+            'pm4ngs-chipexo-demo = pm4ngs.main:chipexo_demo',
+            'pm4ngs-transcriptome-annotation = pm4ngs.main:transcriptome_annotation',
+            'pm4ngs-transcriptome-annotation-demo = pm4ngs.main:transcriptome_annotation_demo'
         ],
     }
 )
diff --git a/src/pm4ngs/main.py b/src/pm4ngs/main.py
index c49af5c..8920489 100644
--- a/src/pm4ngs/main.py
+++ b/src/pm4ngs/main.py
@@ -39,6 +39,16 @@
             'https://raw.githubusercontent.com/ncbi/pm4ngs-chipexo/master'
             '/example/pm4ngs_chipexo_demo_sample_data.csv'
     },
+    4: {
+        'name': 'Transcriptome-Annotation',
+        'url': 'https://github.com/ncbi/pm4ngs-transcriptome-annotation',
+        'example_yml':
+            'https://raw.githubusercontent.com/ncbi/pm4ngs-transcriptome-annotation/master'
+            '/example/pm4ngs_transcriptome_demo_config.yaml',
+        'sample_sheet':
+            'https://raw.githubusercontent.com/ncbi/pm4ngs-transcriptome-annotation/master'
+            '/example/pm4ngs_transcriptome_demo_sample_data.csv'
+    }
 }
 
 
@@ -97,6 +107,14 @@ def chipexo_demo():
     generate_demo(3)
 
 
+def transcriptome_annotation():
+    create_predefined(4)
+
+
+def transcriptome_annotation_demo():
+    generate_demo(4)
+
+
 def create_predefined(pipeline):
     args = command_line(pipeline)
     print('Generating {} data analysis project'.format(