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SeqShop: Sequence Mapping and Assembly Practical, December 2014 (view source)

Revision as of 16:35, 15 May 2015

16 bytes removed ,  16:35, 15 May 2015
→‎Download the example data
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''If you are running during the SeqShop Workshop, please skip this section.''
 
''If you are running during the SeqShop Workshop, please skip this section.''
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
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=== Download the example data ===
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Download and untar file containing the example data used in the practicals:
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mkdir -p ~/seqshop
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cd ~/seqshop
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wget http://csg.sph.umich.edu/mktrost/seqshopExampleDec2014.tar.gz
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tar xvf seqshopExampleDec2014.tar.gz
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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.
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=== Download & Build GotCloud ===
 
=== Download & Build GotCloud ===
 
If you do not already have GotCloud:
 
If you do not already have GotCloud:
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* cd to where you want GotCloud installed (you can change this to any directory you want)
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mkdir -p ~/seqshop
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cd ~/seqshop/
   
* 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:
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  wget https://github.com/statgen/gotcloud/archive/gotcloud.workshopDec2014.tar.gz
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  wget https://github.com/statgen/gotcloud/archive/gotcloud.1.15.tar.gz
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  tar xvf gotcloud.workshopDec2014.tar.gz
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  tar xvf gotcloud.1.15.tar.gz
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  mv gotcloud-gotcloud.workshopDec2014 gotcloud
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  mv gotcloud-gotcloud.1.15 gotcloud
 
  cd gotcloud/src
 
  cd gotcloud/src
 
  make
 
  make
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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.
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  −
=== Download the example data ===
  −
Download and untar file containing the example data used in the practicals:
  −
wget http://www.sph.umich.edu/csg/mktrost/seqshopExampleDec2014.tar.gz
  −
tar xvf seqshopExampleDec2014.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.
      
{{SeqShopRemoteEnv}}
 
{{SeqShopRemoteEnv}}
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''This section is specifically for the SeqShop Workshop computers.''
 
''This section is specifically for the SeqShop Workshop computers.''
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<div class="mw-collapsible" style="width:600px">
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<div class="mw-collapsible mw-collapsed" style="width:600px">
 
''If you are not running during the SeqShop Workshop, please skip this section.''
 
''If you are not running during the SeqShop Workshop, please skip this section.''
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
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</div>
 
</div>
 
</div>
 
</div>
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== Return to Workshop Wiki Page ==
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Return to main workshop wiki page: [[SeqShop: December 2014]]
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/12407...13259"

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