added blast.submit to repository and updated README

README.md

@@ -20,3 +20,8 @@ This submit file executes a corresponding bash script (run_parsnp.sh) with three
 run_parsnp.sh
 -------------
 This is a simple bash script that will unpack the compressed genomes, make and move them into a directory, execute parsnp, and finally compress parsnp's output (a folder containing various files) so that it can be transferred back. 
+
+blast.submit
+------------
+This submit file runs blastp of files named $(PROCESS).tsv against a blast
+database (which is transferred with the jobs).

blast.submit

@@ -0,0 +1,20 @@
+universe = vanilla
+executable = /opt/PepPrograms/ncbi-blast-2.2.31+/bin/blastp
+arguments = "-db coreDB -query $(PROCESS).fasta -outfmt 6 -out $(PROCESS).tsv -num_threads 4"
+
+output = blast_$(PROCESS).out
+error = blast_$(PROCESS).err
+log = blast.log
+
+transfer_executable = NO
+should_transfer_files = YES
+when_to_transfer_output = ON_EXIT
+transfer_input_files = $(PROCESS).fasta,coreDB.phr,coreDB.pin,coreDB.psq
+
+request_cpus = 4
+request_memory = 1GB
+request_disk = 1GB
+
+priority = 1
+
+queue 276