source: trunk/brs2010p35/src/jag/test/vallid_run_check.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: 1.4 KB
Line 
1#!/bin/sh
2#basic function test for JAG
3#system requirments JAG:
4#linux 64 bit or Mac OS X
5#Python (2.4, 2.5 , 2.6 tested (2.7 intial testing succeed ) )
6#system requirments for this test script:
7# curl or wget
8#md5sum (optional)
9
10# test if curl avaible to download the test files
11which curl> /dev/null
12OUT=$?
13set -e
14if [ $OUT -eq 0 ]; then
15  echo "using curl"
16   curl http://brs.nbic.nl/jag.tar.bz2 -o jag.tar.bz2
17else
18  echo "using wget"
19  wget http://brs.nbic.nl/jag.tar.bz2
20fi
21
22#uncompress the test files
23tar -xjf jag.tar.bz2
24#execute jag with most common options
25cd brs2010p35
26echo "step 1"
27./jag --group src/test/total.txt --bfile=src/test/hapmap_CEU_r23_60 --pheno=src/test/pheno60.txt
28echo "step 2"
29./jag --group src/test/total.txt --bfile=src/test/hapmap_CEU_r23_60 --pheno=src/test/pheno60.txt --perm=5 --seed=11
30./jag --group src/test/total.txt --bfile=src/test/hapmap_CEU_r23_60 --pheno=src/test/pheno60.txt --perm=2 --seed=12
31echo "step 3"
32./jag --merge
33echo "step 4"
34./jag --draw 100 --group src/test/total.txt --neff FG2 --data=src/test/all_snps_in_gene_NCBI.txt --bfile=src/test/hapmap_CEU_r23_60 --emp empp.pheno1.out --seed=11
35./jag --draw 100 --group src/test/total.txt --ngenes FG2 --data=src/test/all_snps_in_gene_NCBI.txt --bfile=src/test/hapmap_CEU_r23_60  --seed=11 
36#test that md5sum is avaibble, otherwise skip
37set +e
38which md5sum > /dev/null
39OUT=$?
40set -e
41if [ $OUT -eq 0 ]; then
42  md5sum -c  src/test/checksum.md5
43fi
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