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Revision as of 17:26, 25 June 2014
, 17:26, 25 June 2014→Run GotCloud Align
** 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
* <code>--out_dir</code> tells GotCloud where to write the output.[[File:gcalignStart.png|850px]]
* <code>--out_dir</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:gcalignStart.png|850px]]
This should take 1-3 minutes to run.
This should take 1-3 minutes to run.
