source: trunk/brs2010p35/src/jag/create+test.sh @ 2

Last change on this file since 2 was 2, checked in by tim.te.beek@…, 8 years ago

Add revision 338 snapshot of previous SVN instance, omitting PLINK binaries

File size: 1.0 KB
Line 
1#!/bin/sh
2cd ..
3rm  src/test/checksum.md5
4rm *
5cp src/jag.py jag && chmod +x jag
6echo "step 1"
7./jag --group src/test/total.txt --bfile=src/test/hapmap_CEU_r23_60 --pheno=src/test/pheno60.txt
8
9echo "step 2"
10./jag --group src/test/total.txt --bfile=src/test/hapmap_CEU_r23_60 --pheno=src/test/pheno60.txt --perm=5 --seed=11
11./jag --group src/test/total.txt --bfile=src/test/hapmap_CEU_r23_60 --pheno=src/test/pheno60.txt --perm=2 --seed=12
12echo "step 3"
13./jag --merge
14echo "step 4"
15./jag --draw 100 --group src/test/total.txt --neff FG2 --data=src/test/all_snps_in_gene_NCBI.txt --bfile=src/test/hapmap_CEU_r23_60 --emp empp.pheno1.out --seed=11 
16./jag --draw 100 --group src/test/total.txt --ngenes FG2 --data=src/test/all_snps_in_gene_NCBI.txt --bfile=src/test/hapmap_CEU_r23_60 --emp empp.pheno1.out --seed=11
17
18md5sum  * |grep -v jag |grep -v perm.merged.P2 > src/test/checksum.md5
19rm *
20cp src/jag.py jag && chmod +x jag
21cd ..
22rsync -avz brs2010p35 brs.nbic.nl:/home/maartenk/jag
23#rm jag.tar.bz2
24#tar cfa jag.tar.bz2 brs2010p35/
25
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