add readme for uiuc_igb_scripts

[uiuc_igb_scripts.git] / README.md

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+# Don's Cluster Scripts
+
+This repo contains three tools which you might find useful; but
+really, you probably just want it for `dqsub`.
+
+## dqsub -- qsub or sbatch generator
+
+Use this script to generate qsub scripts. You can run it like:
+
+`dqsub -q default --mem 40G --ppn 12 make foo`
+
+or
+
+`ls -1 */|dqsub -q budget --mem 5 --ppn 6 --array chdir make`
+
+See its documentation for more details.
+
+## fpkm_from_srr
+
+Quick script to get FPKMs from an SRR. Don't actually use this
+anymore.
+
+## run_make
+
+Run make with some wrapper options; mainly useful so you can do
+
+`qsub -v MAKE_OPTS=foo -l ppn:5,mem:40G run_make`
+
+but this is largely superseded by `dqsub`.