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Commit e4e8c9de authored by selva's avatar selva Committed by Selvaganapathy Kannan
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...@@ -35,107 +35,26 @@ If you are self-hosting the BiTIA server, you need `bitia-runner` as well. See ...@@ -35,107 +35,26 @@ If you are self-hosting the BiTIA server, you need `bitia-runner` as well. See
the documents of `bitia-runner` for more details. TODO. the documents of `bitia-runner` for more details. TODO.
## EXAMPLES ## EXAMPLES
1. Using samtools to view a fastq file with same name as provided in url 1. Using samtools to view a fastq file with same name as provided in url
<!--
<div class="tab"> NORMAL PIPELINE EXECUTION CODE | BITIA EXECUTION CODE
<button class="tablinks" onclick="openCity(event, 'London')">Ubuntu</button> :-------------------------:|:-------------------------:
<button class="tablinks" onclick="openCity(event, 'Paris')">Arch</button> ![](./docs/source/img/readme_example_1.gif) |![](./docs/source/img/readme_example_1_bitia.gif)
<button class="tablinks" onclick="openCity(event, 'Tokyo')">BiTIA</button>
</div>
<div id="London" class="tabcontent">
<div id="termynal" data-termynal>
<span data-ty="input">sudo apt get install wget samtools</span>
<span data-ty="input">wget https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq</span>
<span data-ty="input">samtools convert 1_control_18S_2019_minq7%20-%20Copy.fastq</span>
</div>
</div>
<div id="Paris" class="tabcontent">
<div id="termynal1" data-termynal>
<span data-ty="input">pacman -S wget samtools</span>
<span data-ty="input">wget https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq</span>
<span data-ty="input">samtools convert 1_control_18S_2019_minq7%20-%20Copy.fastq</span>
</div>
</div>
<div id="Tokyo" class="tabcontent">
<div id="termynal2" data-termynal>
<span data-ty="input">bitia run "samtools convert &lt;sample.fastq|https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq&gt;"</span>
</div>
</div>
-->
<div class="tab">
<button class="tablinks" onmouseover="openCity(event, 'Ubuntu')">Ubuntu</button>
<button class="tablinks" onmouseover="openCity(event, 'Pacman')">Pacman</button>
<button class="tablinks" onmouseover="openCity(event, 'BiTIA')">BiTIA</button>
</div>
<div id="Ubuntu" style="display: block;" class="tabcontent">
<div id="termynal" data-termynal>
<span data-ty="input">sudo apt get install wget samtools</span>
<span data-ty="input">wget https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq</span>
<span data-ty="input">samtools convert 1_control_18S_2019_minq7%20-%20Copy.fastq</span>
</div>
</div>
<div id="Pacman" style="display: none;"class="tabcontent">
<div id="termynal1" data-termynal>
<span data-ty="input">pacman -S wget samtools</span>
<span data-ty="input">wget https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq</span>
<span data-ty="input">samtools convert 1_control_18S_2019_minq7%20-%20Copy.fastq</span>
</div>
</div>
<div id="BiTIA" style="display: none;" class="tabcontent">
<div id="termynal2" data-termynal>
<span data-ty="input">bitia run "samtools convert &lt;https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq&gt;"</span>
</div>
</div>
<div class="clearfix"></div>
2. Using samtools to view a fastq file with different file name as provided in url 2. Using samtools to view a fastq file with different file name as provided in url
<div class="tab">
<button class="tablinks" onmouseover="openCity(event, 'UBUNTU')">Ubuntu</button>
<button class="tablinks" onmouseover="openCity(event, 'PACMAN')">Pacman</button>
<button class="tablinks" onmouseover="openCity(event, 'BITIA')">BiTIA</button>
</div>
<div id="UBUNTU" style="display: block;" class="tabcontent">
<div id="termynal3" data-termynal>
<span data-ty="input">sudo apt get install wget samtools</span>
<span data-ty="input">wget sample.fastq https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq</span>
<span data-ty="input">samtools convert sample.fastq</span>
</div>
</div>
<div id="PACMAN" style="display: none;"class="tabcontent">
<div id="termynal4" data-termynal>
<span data-ty="input">pacman -S wget samtools</span>
<span data-ty="input">wget sample.fastq https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq</span>
<span data-ty="input">samtools convert sample.fastq</span>
</div>
</div>
<div id="BITIA" style="display: none;" class="tabcontent">
<div id="termynal5" data-termynal>
<span data-ty="input">bitia run "samtools convert &lt;sample.fastq|https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq&gt;"</span>
</div>
</div>
<div class="clearfix"></div>
<script type="text/javascript" src="https://raw.githack.com/Ganz1285/termynal/master/termynal.js" data-termynal-container="#termynal|#termynal1|#termynal2|#termynal3|#termynal4|#termynal5"></script>
NORMAL PIPELINE EXECUTION CODE | BITIA EXECUTION CODE
:-------------------------:|:-------------------------:
![](./docs/source/img/readme_example_2.gif) |![](./docs/source/img/readme_example_2_bitia.gif)
3. Using Fastqc to do Quality check on a fastq file with same file name as provided
NORMAL PIPELINE EXECUTION CODE | BITIA EXECUTION CODE
:-------------------------:|:-------------------------:
![](./docs/source/img/readme_example_3.gif) |![](./docs/source/img/readme_example_3_bitia.gif)
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