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

Revision as of 16:35, 15 May 2015

347 bytes added ,  16:35, 15 May 2015
→‎Download the example data
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== Introduction ==
 
== Introduction ==
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See the [[Media:SeqShop - GotCloud Align.pdf|introductory slides]] for an intro to this tutorial.
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Main Workshop wiki page: [[SeqShop: December 2014]]
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 +
See the [[Media:Dec2014 SeqShop - GotCloud Align.pdf|introductory slides]] for an intro to this tutorial.
    
== Goals of This Session ==
 
== Goals of This Session ==
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== Setup in person at the SeqShop Workshop ==
 
== Setup in person at the SeqShop Workshop ==
 
''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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* Tutorial input files
 
* Tutorial input files
 
* Setup an output directory
 
* Setup an output directory
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  source /home/mktrost/seqshop/setup.txt
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  source /net/seqshop-server/home/mktrost/seqshop/setup.txt
 
* You won't see any output after running <code>source</code>
 
* You won't see any output after running <code>source</code>
 
** It silently sets up your environment
 
** It silently sets up your environment
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 +
Look at setup.txt
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cat /net/seqshop-server/home/mktrost/seqshop/setup.txt
 
<div class="mw-collapsible mw-collapsed" style="width:200px">
 
<div class="mw-collapsible mw-collapsed" style="width:200px">
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View setup.txt
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* setup.txt screenshot
 
<div class="mw-collapsible-content">
 
<div class="mw-collapsible-content">
 
[[File:setup.png|500px]]
 
[[File:setup.png|500px]]
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== Setup when running on your own outside of the SeqShop Workshop ==
 
== Setup when running on your own outside of the SeqShop Workshop ==
 
''This section is specifically for running on your own outside of the SeqShop Workshop.''
 
''This section is specifically for running on your own outside of the SeqShop Workshop.''
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<div class="mw-collapsible mw-collapsed" style="width:600px">
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<div class="mw-collapsible" style="width:600px">
 
''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.workshop.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.workshop.tar.gz
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  tar xvf gotcloud.1.15.tar.gz
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  mv gotcloud-gotcloud.workshop 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:
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wget http://www.sph.umich.edu/csg/mktrost/seqshopExample.tar.gz
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tar xvf seqshopExample.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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</div>
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</div>
    
== Examining [[GotCloud]] Align Input Files ==
 
== Examining [[GotCloud]] Align Input Files ==
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Now that we have all of our input files, we need just a simple command to run them
 
Now that we have all of our input files, we need just a simple command to run them
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  ${GC}/gotcloud align --conf ${SS}/gotcloud.conf --numjobs 2 --base_prefix ${SS} --outdir ${OUT}
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* When running at home if you don't have 4 CPUs, reduce the <code>--numjobs</code> setting (it will take longer to run).
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  ${GC}/gotcloud align --conf ${SS}/gotcloud.conf --numjobs 4 --base_prefix ${SS} --outdir ${OUT}
    
* <code>${GC}/gotcloud</code> runs GotCloud
 
* <code>${GC}/gotcloud</code> runs GotCloud
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* <code>--conf</code> tells GotCloud the name of the configuration file to use.
 
* <code>--conf</code> tells GotCloud the name of the configuration file to use.
 
** The configuration for this test was downloaded with the seqshop input files.
 
** The configuration for this test was downloaded with the seqshop input files.
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* <code>--numjobs</code> means to run 2 samples at a time.
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* <code>--numjobs</code> means to run 4 samples at a time.
 
** How many you can run concurrently depends on your system.
 
** How many you can run concurrently depends on your system.
 
* <code>--base_prefix</code> tells GotCloud the prefix to append to relative paths.
 
* <code>--base_prefix</code> tells GotCloud the prefix to append to relative paths.
 
** The Configuration file cannot read environment variables, so we need to tell GotCloud the path to the input files, ${SS}
 
** The Configuration file cannot read environment variables, so we need to tell GotCloud the path to the input files, ${SS}
 
** Alternatively, gotcloud.conf could be updated to specify the full paths
 
** Alternatively, gotcloud.conf could be updated to specify the full paths
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* <code>--out_dir</code> tells GotCloud where to write the output.
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* <code>--outdir</code> tells GotCloud where to write the output.
 
** This could be specified in gotcloud.conf, but to allow you to use the ${OUT} to change the output location, it is specified on the command-line
 
** This could be specified in gotcloud.conf, but to allow you to use the ${OUT} to change the output location, it is specified on the command-line
   −
[[File:gcalignStartNew.png|850px]]
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[[File:gcalignStartNew.png|650px]]
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This should take 1-3 minutes to run.
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This should take about 1 minute to run.
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It should end with a line like: <code>Processing finished in 47 secs with no errors reported</code>
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It should end with a line like: <code>Processing finished in 54 secs with no errors reported</code>
 
* The <code>WARNING</code> messages are just to let you know that the default Read Group field settings are being used.
 
* The <code>WARNING</code> messages are just to let you know that the default Read Group field settings are being used.
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''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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To logout of seqshop1/2/3/4, type:
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exit
 
To logout of seqshop-server, type:
 
To logout of seqshop-server, type:
 
  exit
 
  exit
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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/12034...13259"

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