[Swift-commit] r2793 - in usertools/cio: . science science/blast

[noreply at svn.ci.uchicago.edu]

Author: aespinosa
Date: 2009-03-31 20:26:56 -0500 (Tue, 31 Mar 2009)
New Revision: 2793

Added:
   usertools/cio/science/
   usertools/cio/science/blast/
   usertools/cio/science/blast/mockblast.sh
   usertools/cio/science/blast/runblast.sh
   usertools/cio/science/blast/test.in
Log:
Created science directory.  Initial tests for real blast and mock blast

Added: usertools/cio/science/blast/mockblast.sh
===================================================================
--- usertools/cio/science/blast/mockblast.sh	                        (rev 0)
+++ usertools/cio/science/blast/mockblast.sh	2009-04-01 01:26:56 UTC (rev 2793)
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+
+DB=/disks/ci-gpfs/swift/blast/pir/UNIPROT_for_blast_14.0.seq.*
+
+for i in $DB; do
+  dd if=$i of=/dev/null bs=1M
+done
+sleep 18


Property changes on: usertools/cio/science/blast/mockblast.sh
___________________________________________________________________
Name: svn:executable
   + *

Added: usertools/cio/science/blast/runblast.sh
===================================================================
--- usertools/cio/science/blast/runblast.sh	                        (rev 0)
+++ usertools/cio/science/blast/runblast.sh	2009-04-01 01:26:56 UTC (rev 2793)
@@ -0,0 +1,6 @@
+
+DB=/disks/ci-gpfs/swift/blast/pir/UNIPROT_for_blast_14.0.seq
+strace -tt -ff -o traceblast \
+    /home/aespinosa/science/blast/ncbi.communicado/bin/blastall -p blastp -F F \
+    -d $DB -i test.in -v 300 -b 300 -m8 -o test.out
+  

Added: usertools/cio/science/blast/test.in
===================================================================
--- usertools/cio/science/blast/test.in	                        (rev 0)
+++ usertools/cio/science/blast/test.in	2009-04-01 01:26:56 UTC (rev 2793)
@@ -0,0 +1,5 @@
+>A0AQI4
+VWLRRCTHYLFIVVVAVNSTLLTINAGDYIFYTDWAWTSYTVFSISQTLMLIVGATYYLT
+FTGVPGTATYYALIMTVYTWIAKAAWFSLGYPYDFIVTPVWLPSAMLLDLVYWATKKNKH
+SLILFGGVLVGMSLPLSNMVNLITVADPLETAFKYPRPTLPPYMTPIEPQVGKFYNSPVA
+LGAGAGAVLGCTFAALGCKLNTWTYR