Differences

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--- mpiblast [2010/01/19 06:31] – 172.26.0.166
+++ mpiblast [2010/01/19 09:38] – 172.26.0.166
@@ Line 9: / Line 9: @@
   * **nfrags** specifies how many database fragments you want to split the original database into. This should be equal to how many different nodes you want to run mpiblast on.
-http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl
-===== Updating BLAST Databases =====
-http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastdb.html
 ===== Notes on .ncbirc ====
 Notes on setting up the ''~/.ncbirc'' file from the mpiBLAST installation page: http://www.mpiblast.org/Docs/Install#unix
@@ Line 62: / Line 59: @@
 The number of processes for an MPI job should be +1 of the number of CPUs because one process is used as the master to control the other jobs.
 ===== Links =====
-Submitting MPI jobs using SGE: http://www.shef.ac.uk/wrgrid/documents/gridengine.html
+  * Submitting MPI jobs using SGE: http://www.shef.ac.uk/wrgrid/documents/gridengine.html
+  * mpiBLAST Guide: http://www.mpiblast.org/Docs/Guide
+  * Updating the BLAST databases: http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl
+<code>$ sudo mkdir -p /state/
+$ sudo ln -s /scratch/ /state/partition1
+$ sudo chmod 777 /scratch/
+$ sudo chmod o+t /scratch/</code>