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| 5. Run gotcloud with zero jobs to generate a Makefile. | | 5. Run gotcloud with zero jobs to generate a Makefile. |
− | : <code>/path/to/gotcloud/gotcloud snpcall --conf /path/to/configuration.conf --numjobs 0</code> | + | : <code style="background:#f0f0f0">/path/to/gotcloud/gotcloud snpcall --conf /path/to/configuration.conf --numjobs 0</code> |
| :* The newly generated Makefile will be located in the directory <code>OUT_DIR</code> that is specified in your configuration file. It will be named <code>umake.snpcall.Makefile</code>. | | :* The newly generated Makefile will be located in the directory <code>OUT_DIR</code> that is specified in your configuration file. It will be named <code>umake.snpcall.Makefile</code>. |
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| :* If you're in a hurry to finish your pipeline, you can find an email address that will text the emails to your phone. Only use that in the second script, though! | | :* If you're in a hurry to finish your pipeline, you can find an email address that will text the emails to your phone. Only use that in the second script, though! |
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− | 8. Figure out the name of the Flux account that you're going to use. You can see which Flux accounts you have access to by running <code>mdiag -u $USER</code> and looking at the list after <code>ALIST</code>. | + | 8. Figure out the name of the Flux account that you're going to use. You can see which Flux accounts you have access to by running <code style="background:#eee;white-space:nowrap">mdiag -u $USER</code> and looking at the list after <code>ALIST</code>. |
| :* Eg, <code>sph_flux</code> | | :* Eg, <code>sph_flux</code> |
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− | 9. Figure out how many processors you're going to use at once. Run <code>mdiag -a YOU_FLUX_ACCOUNT</code>. I recommend running <code>MAXPROC</code> + <code>MAXIJOB[USER]</code> many jobs. <code>MAXPROC</code> is the number of processors on your account, and <code>MAXIJOB[USER]</code> is the number of jobs that can sit idle in the queue waiting to be run (often 20). | + | 9. Figure out how many processors you're going to use at once. Run <code style="background:#eee;white-space:nowrap">mdiag -a YOU_FLUX_ACCOUNT</code>. I recommend running <code>MAXPROC</code> + <code>MAXIJOB[USER]</code> many jobs. <code>MAXPROC</code> is the number of processors on your account, and <code>MAXIJOB[USER]</code> is the number of jobs that can sit idle in the queue waiting to be run (often 20). |
| :* This number will usually be between 20 and 1000. | | :* This number will usually be between 20 and 1000. |
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| 10. Figure out which steps to run first. The steps go in the order glfN, vcfN, pvcfN, filtN, svmN, splitN, allN where N is the name of a chromosome (ie, 1-22 and maybe X and Y). If you skip a step, it's not a problem, because <code>make</code> will run it for you. If you're confident that everything will work beautifully, you can go straight to the step <code>allN</code> (or just <code>all</code> as a shortcut). | | 10. Figure out which steps to run first. The steps go in the order glfN, vcfN, pvcfN, filtN, svmN, splitN, allN where N is the name of a chromosome (ie, 1-22 and maybe X and Y). If you skip a step, it's not a problem, because <code>make</code> will run it for you. If you're confident that everything will work beautifully, you can go straight to the step <code>allN</code> (or just <code>all</code> as a shortcut). |
− | :* For example, I used <code>glf1 glf2 glf3 glf4 glf5 glf6 glf7 glf8 glf9 glf10 glf11 glf12 glf13 glf14 glf15 glf16 glf17 glf18 glf19 glf20 glf21 glf22 </code> the first time I ran on Flux. Then I ran <code>vcf1 vcf2...</code>, and on down the list until finally <code>all</code>. | + | :* For example, I used <code style="background:#eee;white-space:nowrap">glf1 glf2 glf3 glf4 glf5 glf6 glf7 glf8 glf9 glf10 glf11 glf12 glf13 glf14 glf15 glf16 glf17 glf18 glf19 glf20 glf21 glf22 </code> the first time I ran on Flux. Then I ran <code>vcf1 vcf2...</code>, and on down the list until finally <code>all</code>. |
− | :* Feel free to use the script <code>perl -e 'print "glf$_ " for 1..22'</code> to mitigate repetitive strain injuries. | + | :* Feel free to use the script <code style="background:#eee;white-space:nowrap">perl -e 'print "glf$_ " for 1..22'</code> to mitigate repetitive strain injuries. |
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| 11. Inside that new folder, make a new file named <code>pbs.options</code> that contains the following: | | 11. Inside that new folder, make a new file named <code>pbs.options</code> that contains the following: |
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| ===Finally, submit your jobs=== | | ===Finally, submit your jobs=== |
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− | 13. Run <code>qsub script_thats_in_charge.sh</code>. It's important that you run this in the same folder where <code>pbs.options</code> lives. | + | 13. Run <code style="background:#eee;white-space:nowrap">qsub script_thats_in_charge.sh</code>. It's important that you run this in the same folder where <code>pbs.options</code> lives. |
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| 14. Once that finishes, if any steps remain, then update YOUR_MAKEFILE_TARGETS_FROM_STEP_10 and go back to step 13. | | 14. Once that finishes, if any steps remain, then update YOUR_MAKEFILE_TARGETS_FROM_STEP_10 and go back to step 13. |
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| ==How to monitor your jobs on Flux== | | ==How to monitor your jobs on Flux== |