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Revision as of 16:57, 12 August 2013
, 16:57, 12 August 2013→Fetch the Tar Releases
<code>
<code>
# The easiest way:
# The easiest way:
<b>wget --retr-symlinks ftp://share.sph.umich.edu/gotcloud/gotcloud\*latest\*.tgz</b>
<b>wget --retr-symlinks ftp://share.sph.umich.edu/gotcloud/gotcloud-\*latest\*.tgz</b>
# Another way:
# Another way:
ftp> <b>cd gotcloud</b>
ftp> <b>cd gotcloud</b>
250 Directory successfully changed.
250 Directory successfully changed.
ftp> <b>mget gotcloud*latest*.tgz</b>
ftp> <b>mget gotcloud-*latest*.tgz</b>
ftp> <b>quit</b>
ftp> <b>quit</b>
221 Goodbye.
221 Goodbye.
</code>
====Unpack the Tar Release====
Unpack the realeases:
tar xf gotcloud-*latest*.tgz
===Testing the GotCloud Installation===
We recommend that at least the first time, you download the test packages so you can
conveniently test the installation and make sure everything runs smoothly.
The tests run within a few minutes and are self checking, so unless you see obvious errors,
you can be reasonably sure everything is set up properly.
You only need to do this once, unless you have made significant changes to your Unix system.
The test case results are self-checked and if errors should occur, it will be obvious.
<code>
# Test the aligner (3 minutes +/- 1 minute)
'''gotcloud/bin/gotcloud align --test ~/testalign'''
Removing any previous results from: /home/myuser/testalign/aligntest
Running GOTCLOUD TEST, test log in: /home/myuser/testalign/aligntest.log
Created /home/myuser/testalign/aligntest/Makefiles/align_Sample2.Makefile
Created /home/myuser/testalign/aligntest/Makefiles/align_Sample1.Makefile
---------------------------------------------------------------------
Waiting while samples are processed...
Processing finished in 63 secs with no errors reported
Results from DIFF will be in /home/myuser/testalign/diff_logfiles_results.txt
Successful comparison of data in '/home/myuser/testalign/aligntest' and 'gotcloud/test/align/expected/aligntest'
Successfully ran the test case, congratulations!
'''rm -rf ~/testalign''' # If no error
# Test snp calling (7 minutes +/-2 minute)
'''gotcloud/bin/gotcloud snpcall --test ~/testsnp'''
Removing any previous results from: /home/myuser/testsnp/umaketest
Running GOTCLOUD TEST, test log in: /home/myuser/testsnp/umaketest.log
Results from DIFF will be in /home/myuser/testsnp/diff_logfiles_results_umake.txt
Successful comparison of data in '/home/myuser/testsnp/umaketest' and 'gotcloud/test/umake/expected/umaketest'
Successfully ran the test case, congratulations!
'''rm -rf ~/testsnp''' # If no error
</code>
</code>
