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r78v10a07 committed Jul 15, 2021
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21 changes: 2 additions & 19 deletions docs/source/pipelines/transcriptomeAnnotationPipeline.rst
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Expand Up @@ -6,7 +6,7 @@ Transcriptome Annotation pipeline for non-model organisms

.. ATTENTION::

This annotation pipeline uses Google Cloud platform for all computing demand tasks. Users should have installed
This annotation pipeline uses Google Cloud platform for all computing tasks. Users should have installed
and configured `Cloud SDK`_.

GCP configuration
Expand All @@ -28,23 +28,6 @@ It can be installed:
localhost:~> gcloud components install kubectl
Elastic-Blast
-------------

Elastic-blast should be aslo installed in the host machine.

It can be installed in a Python virtual environment:

.. code-block:: bash
localhost:~> pip install elastic-blast
Or using Conda:

.. code-block:: bash
localhost:~> conda install elastic-blast
Input requirements
------------------

Expand Down Expand Up @@ -123,7 +106,7 @@ The **pm4ngs-rnaseq** command line will create a project structure as:
│   ├── 01 - Download and pre-processing quality control.ipynb
│   ├── 02 - Sample Trimming.ipynb
│   ├── 03 - Vector removal.ipynb
│   ├── 04 - Detecting Contamination with Elastic-Blast.ipynb
│   ├── 04 - Detecting Contamination.ipynb
│   ├── 05 - Trinity assembly.ipynb
│   ├── 06 - Vector Detection and data Partitioning.ipynb
│   ├── 07 - Transcriptome annotation.ipynb
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