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Revision as of 03:00, 28 January 2016
, 03:00, 28 January 2016→Logging Off
Main Workshop wiki page: [[SeqShop: May 2015]]
Main Workshop wiki page: [[SeqShop: May 2015]]
See the [[Media:Dec2014 SeqShop - GotCloud Align.pdf|introductory slides]] for an intro to this tutorial.
See the [[Media:May2015 SeqShop - GotCloud Align.pdf|introductory slides]] for an intro to this tutorial.
== Goals of This Session ==
== Goals of This Session ==
** How to visualize sequence data to examine the reads aligned to particular genomic positions
** How to visualize sequence data to examine the reads aligned to particular genomic positions
== Setup in person at the SeqShop Workshop ==
== Setup ==
''The section below is specifically for the Michigan SeqShop Workshop computers.''
<div class="mw-collapsible mw-collapsed">
''If you are using a SeqShop computer, please expand this section.''
<div class="mw-collapsible mw-collapsed" style="width:200px">
<div class="mw-collapsible-content">
<div class="mw-collapsible-content">
{{SeqShopLoginA}}
</div>
</div>
</div>
</div>
=== Download the example data ===
=== Download the example data ===
mkdir -p ~/seqshop
mkdir -p ~/seqshop
cd ~/seqshop
cd ~/seqshop
wget http://www.sph.umich.edu/csg/mktrost/seqshopExampleDec2014.tar.gz
wget http://csg.sph.umich.edu/mktrost/seqshopExampleMay2015.tar.gz
tar xvf seqshopExampleDec2014.tar.gz
tar xvf seqshopExampleMay2015.tar.gz
You will see the names of all the files included in the example data scrolling on the screen as they are unpacked from the tar file.
You will see the names of all the files included in the example data scrolling on the screen as they are unpacked from the tar file.
If you do not already have GotCloud:
If you do not already have GotCloud:
* download, decompress, and build the version of gotcloud that was tested with this tutorial:
* download, decompress, and build the version of gotcloud that was tested with this tutorial:
wget https://github.com/statgen/gotcloud/archive/gotcloud.1.17.tar.gz
wget https://github.com/statgen/gotcloud/archive/gotcloud.1.17.4.tar.gz
tar xvf gotcloud.1.17.tar.gz
tar xvf gotcloud.1.17.4.tar.gz
mv gotcloud-gotcloud.1.17 gotcloud
mv gotcloud-gotcloud.1.17.4 gotcloud
cd gotcloud/src
cd gotcloud/src
make
make -j 3
cd ../..
cd ../..
Remember the path to gotcloud/ that is what you will need to set your GC variable to.
Remember the path to gotcloud/ that is what you will need to set your GC variable to.
{{SeqShopRemoteEnv}}
''This section is specifically for the SeqShop Workshop computers.''
<div class="mw-collapsible mw-collapsed" style="width:600px">
''If you are using a SeqShop computer, please expand this section.''
<div class="mw-collapsible-content">
{{SeqShopLoginSubMachine}}
</div>
</div>
</div>
</div>
{{SeqShopRemoteEnv}}
== Examining [[GotCloud]] Align Input Files ==
== Examining [[GotCloud]] Align Input Files ==
''This section is specifically for the SeqShop Workshop computers.''
''This section is specifically for the SeqShop Workshop computers.''
<div class="mw-collapsible mw-collapsed" style="width:600px">
<div class="mw-collapsible mw-collapsed">
''If you are not running during the SeqShop Workshop, please skip this section.''
''If you are running on a SeqShop computer, please expand this section.''
<div class="mw-collapsible-content">
<div class="mw-collapsible-content">
To logout of seqshop1/2/3/4, type:
To logout of seqshop1/2/3/4, type:
== Return to Workshop Wiki Page ==
== Return to Workshop Wiki Page ==
Return to main workshop wiki page: [[SeqShop: December 2014]]
Return to main workshop wiki page: [[SeqShop: May 2015]]
