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GenomeStrip is currently included in with the seqshop example data under the svtoolkit directory. We have added the bin/ sub-directory to add a high level pipeline that will run genomestrip in the same framework as GotCloud.
GenomeStrip is currently included in with the seqshop example data under the svtoolkit directory. We have added the bin/ sub-directory to add a high level pipeline that will run genomestrip in the same framework as GotCloud.
== Setup in person at the SeqShop Workshop ==
== Setup ==
''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">
''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.''
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<div class="mw-collapsible-content">
{{SeqShopLogin}}
{{SeqShopLogin}}
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</div>
</div>
</div>
== Setup when running on your own outside of the SeqShop Workshop ==
=== Prerequisite Tutorials ===
This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]]
This tutorial builds on the alignment tutorial, if you have not already, please first run that tutorial: [[SeqShop:_Sequence_Mapping_and_Assembly_Practical|Alignment Tutorial]]
It also uses the bam.index file created in the SnpCall Tutorial. If you have not yet run that tutorial, please follow the directions at: [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical#GotCloud_BAM_Index_File|GotCloud BAM Index File]]
It also uses the bam.index file created in the SnpCall Tutorial. If you have not yet run that tutorial, please follow the directions at: [[SeqShop:_Variant_Calling_and_Filtering_for_SNPs_Practical#GotCloud_BAM_Index_File|GotCloud BAM Index File]]
{{SeqShopRemoteEnv}}
This is the same setup you did for the previous tutorial, but you need to redo it each time you log in.
== Examining GotCloud/GenomeSTRiP Input files ==
== Examining GotCloud/GenomeSTRiP Input files ==
