1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
|
--------------------------------------------------------------------------------
SAND: simple overlapping (candidate selection / alignment) example
--------------------------------------------------------------------------------
The example included here produces OVL records describing the results
of the overlapping step for a very small assembly. The example is
executed as a script (test_example.sh) that will generate a list of
candidate pairs and then run a sample alignment on each pair in the
list. The resulting OVL records are compared against a correct key as
verification.
The following will explain how to run the example, and describe the
common execution steps included in the example script.
Setup and Execution
-------------------
The example script is meant to be run in-place. Once the
CCTools have been made, it can be executed simply as:
./test_example.sh
--The example script converts a small set of sequences into the
compressed fasta-like format used by the SAND modules.
--The example script starts a worker running on localhost,
looking for a master on localhost port 9091. If that port is in use,
change the example to use a free port.
--The example script next starts the filter_master process, which controls
the candidate selection workload execution. The master takes several
options (here 10 subsets to filter, port 9091, and binary data mode)
and two mandatory arguments: the sequence library, and an output
target candidate file. For more on options, run: filter_master -h
--The worker from the candidate selection is forcibly killed, so the
example script starts another worker running on localhost,
looking for a master on localhost port 9091. If that port is in use,
again, change the example to use a free port.
--The example script next starts the master process, which controls
the alignment workload execution. The master takes several options
(here 1 candidate per Work Queue task, and port 9091) and four
mandatory arguments: the serial alignment executable to run, the
candidate list, the sequence library, and an output target. For more
on options, run: sand_align -h
--Once the master process has completed, the output is compared
against a correct version of the OVL results, and the example
script waits for the worker to time-out.
--The created files are then deleted (with the option to keep the results)
--------------------------------------------------------------------------------
|
