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, 11:10, 26 June 2014
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| Now that we have all of our input files, we need just a simple command to run: | | Now that we have all of our input files, we need just a simple command to run: |
| ${GC}/gotcloud snpcall --conf ${SS}/gotcloud.conf --numjobs 4 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT} | | ${GC}/gotcloud snpcall --conf ${SS}/gotcloud.conf --numjobs 4 --region 22:36000000-37000000 --base_prefix ${SS} --outdir ${OUT} |
| + | * <code>${GC}/gotcloud</code> runs GotCloud |
| + | * <code>align</code> tells GotCloud you want to run the alignment pipeline. |
| + | * <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. |
| * --numjobs tells GotCloud how many jobs to run in parallel | | * --numjobs tells GotCloud how many jobs to run in parallel |
| ** Depends on your system | | ** Depends on your system |
| * --region 22:36000000-37000000 | | * --region 22:36000000-37000000 |
| ** The sample files are just a small region of chromosome 22, so to save time, we tell GotCloud to ignore the other regions | | ** The sample files are just a small region of chromosome 22, so to save time, we tell GotCloud to ignore the other regions |
| + | * <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} |
| + | ** Alternatively, gotcloud.conf could be updated to specify the full paths |
| + | * <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 |
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| <div class="mw-collapsible mw-collapsed" style="width:500px"> | | <div class="mw-collapsible mw-collapsed" style="width:500px"> |