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graphclust_tutorial.yaml
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graphclust_tutorial.yaml
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name: GraphClust workflow
description: Simple instructions for using GraphClust workflow for clustering RNA sequences
title_default: "<b>GraphClust</b>"
tags:
- "GraphClust"
steps:
- title: "<b>A tutorial on Galaxy-GraphClust(Clustering RNA sequences)</b>"
content: "This tour will walk you through the process of <b>GraphClust</b> to cluster RNA sequences.<br><br>
In the forthcoming windows please read and follow the instructions before clicking <b>'Next'</b>.<br><br>
Click <b>'Prev'</b> in case you missed out on any step."
backdrop: true
- title: "<b>A tutorial on GraphClust</b>"
content: "Together we will go through the following steps:<br>
<ol>
<b>
<li>Data Acquisition</li>
<li>Running the Workflow</li>
<li>Understanding the Output</li>
</b>
</lo>"
backdrop: true
- title: "<b>Log in</b>"
element: '#user > li > a'
intro: " To be able to use workflows you should be logged in. So if you already have an account
simply <b>log in</b> or otherwise <b>register</b> by clicking on <b>'User'</b>.<br>
Within a <b>Docker</b> Galaxy-GraphClust everyone can register by default.
<br>
To have a convenient access the worklows <b>log in</b> you can login with the pre-configured username and password: <br>
<b>
username : [email protected]<br>
password : admin<br>
</b>"
position: "left"
- title: "<b>GraphClust</b>"
intro: "Now that you are logged-in we can continue our tour"
position: "left"
backdrop: true
- title: "<b>Create a new history</b>"
element: '#history-options-button'
intro: "Let's start by creating a new history:<br>
<b>(History options :: Create New)</b>"
position: "left"
preclick:
- '#center-panel'
- title: "<b>Rename the history</b>"
element: "#current-history-panel > div.controls"
intro: "Change the name of the new history to <b>'GraphClust'</b>."
position: "left"
- title: "<b>Data Acquisition</b>"
content: "We start with uploading a simple small set of sequences in <b>FASTA</b> format.<br><br>
You will get one FASTA file with RNA sequences that we want to cluster.<br><br>"
backdrop: true
- title: "<b>Data Acquisition</b>"
element: ".upload-button"
intro: "We will import the FASTA file into the history we just created.<br><br>
Click <b>'Next'</b> and the tour will take you to the Upload screen."
position: "right"
postclick:
- ".upload-button"
- title: "<b>Data Acquisition</b>"
element: "button#btn-new"
intro: "The sample input data available on GitHub is a good place to start.<br><br>
Simply click <b>'Next'</b> and the links to the input data will be automatically inserted and ready for upload.<br><br>
Later on, when you want to upload other data, you can do so by clicking the <b>'Paste/Fetch Data'</b> button or
<b>'Choose local file'</b> to upload locally stored file."
position: "top"
postclick:
- "button#btn-new"
- title: "<b>Data Acquisition</b>"
element: ".upload-text-content:first"
intro: "Link acquired !<br><br>
This file contains annotated RNAs with human origin from RFAM database, from a mixture of RNA families."
position: "top"
textinsert:
https://github.com/BackofenLab/docker-galaxy-graphclust/raw/master/data/Rfam-cliques-dataset/cliques-low-representatives.fa
- title: "<b>Data Acquisition</b>"
element: "button#btn-start"
intro: "Click on <b>'Start'</b> to upload the data into your Galaxy history."
position: "top"
- title: "<b>Data Acquisition</b>"
element: "button#btn-close"
intro: "The upload may take awhile.<br><br>
Hit the <b>close</b> button when you see that the files are uploaded into your history."
position: "top"
- title: "<b>Data Acquisition</b>"
element: "#current-history-panel > div.controls"
intro: "You've now acquired the input data. Now let's launch a flavor of <b>Galaxy-GraphClust Workflow</b>.<br><br>"
position: "left"
- title: "<b>Running a Workflow</b>"
element: 'a[href$="/workflow/list_for_run"]'
intro: "Click on <b>'All Workflows'</b> to access your saved and pre-configured Workflows.<br>
Alternatively you can click on <b>'Workflow'</b> tab from the top panel."
position: "right"
- title: "<b>Running a Workflow</b>"
element: 'a[href$="/workflow/run?id=1cd8e2f6b131e891"]'
intro: "Inside your workflows list you should see variations of Galaxy-GraphClust.
The round number specifies the number of iterative clusterings.<br><br>
<b>Click on GraphClust_1_round then Run</b>, which is the faster one better fitting for
the purpose of this tutorial.<b>Then click Next.</b>"
position: "top"
- title: "<b>Running a Workflow</b>"
element: "#field-uid-1 > div.btn-group.ui-radiobutton"
intro: "We skip <b>'History Options'</b> section because we have already created new history, so there is no need to crate a new one.<br><br>"
position: "top"
- title: "<b>Running a Workflow</b>"
element: "#uid-23 > div.portlet-header > div.portlet-title > span > b"
intro: "<b>Step 1</b> is the first step of our workflow. Here an input dataset must be assigned.<br>
Input data is a set of putative RNA sequences that we want to cluster.<br> <br>
Please ensure the fasta file uploaded in the first step is selected."
position: "right"
- title: "<b>Running a Workflow</b>"
element: 'button#uid-11'
intro: "To run the workflow with <b>default setting</b> simply click on <b>'Run workflow'</b> blue button
on the top right.<br>
For details about pipeline settings you can check 'step-by-step' tutorial and Galaxy-GraphClust documentations. <br>"
position: "left"
- title: "<b>Understanding the Output</b>"
intro: "Running the workflow takes a few minutes. The workflow is finished
when all the steps inside History panel changes from gray/yellow to green.<br><br>
After all the steps are done, clustering output is ready.
The results can be checked from navigating through History panel."
position: "top"
- title: "<b>Understanding the Output</b>"
element: "#current-history-panel"
intro: "<b>'cluster.final.stat'</b> file contains overall information about predicted clusters.
<br> By clicking on the <b>'eye'</b> icon you can see the content of the file.<br><br>
The first four columns specify number of clusters, cluster ids, number of sequences in each cluster."
position: "left"
- title: "<b>Understanding the Output</b>"
element: "#current-history-panel"
intro: "Click <b>'CLUSTERS'</b> dataset collection to see clustered sequences.
There is one file for each cluster. <br>
Each file contains information about sequences in that cluster. Each line in the file contains:
<ol>
<li> <b>CLUSTER</b>: cluster number</li>
<li> cm_score: Covariance model bit score indicates how well sequence matches to the CM
model of the cluster.</li>
<li> sequence origin (whether it orginnates from dense center <b>MODEL</b>
or from Infernal <b>CMSEARCH</b> or preclustering <b>CDHIT</b>)</li>
<li>Input fasta sequence id seperated into <b>ORIGID</b> and <b>ORIGHEAD</b> sections</li>
</b>
</ol>"
position: "left"
- title: "<b>A tutorial on GraphClust workflow</b>"
intro: "Thank You for going through our tutorial."
backdrop: true