-
Notifications
You must be signed in to change notification settings - Fork 0
/
RUNNING_SFOLD
93 lines (76 loc) · 3.24 KB
/
RUNNING_SFOLD
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
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
Sfold Executable Code for Academic Users, Version 2.2
=====================================================
-------------
License Terms
-------------
The Sfold Executable Code for Academic Users is a software for
statistical folding and rational design of nucleic acids. Use of this
program is restricted to non-commercial internal research only. Please
read the license agreement (located at ./license/SFOLD-ACADEMIC-LICENSE.html
from your extracted package) before using this program. For more
information about our software, please visit us online at
http://sfold.wadsworth.org/ .
------------
Requirements
------------
The Sfold Executable Code currently runs on Linux (i386/x86_64).
To run the Sfold Executable Code, you will need to have the following
software and libraries installed in your system:
- The R Project for Statistical Computing (http://www.r-project.org/)
- Perl (http://www.perl.org/)
-------------
Running Sfold
-------------
1. Decompress the downloaded Sfold package:
gunzip -c sfold-2.2.tar.gz | tar xvf -
2. Change to the extracted directory:
cd sfold-2.2
3. Configure environment settings:
./configure
A common problem is that R is not found. One easy solution is
to make sure that the "R" binary is in your PATH.
4. Inspect ./sfoldenv to make sure the automatically determined
settings look right to you. If the configure script cannot
locate some of the external programs, e.g. R, you can manually
set the corresponding variable in ./sfoldenv .
5. Test your copy of Sfold by running:
./testsfold/testrun
The test compares results generated by your copy of Sfold to
those from our development machine. If the test fails, check
the indicated log file for more information.
This test takes about 15 seconds on our test system. If it takes
longer than 3 minutes with no response, it may be that R
cannot be run. End the test and
check what happens when you try to run "R" at the command line.
You should see R version information followed by a > command
prompt. Type q() to quit R.
If you get any error messages when trying to run R alone, you
should resolve these first.
6. Execute Sfold:
./bin/sfold
Running ./bin/sfold without any argument will give you the
help message on how to run the program. You can run Sfold
from anywhere in your system.
------------
Output Files
------------
The Sfold program generates numerous text output files.
sfold.out and sclass.out in your output directory save the
general messages from standard output/error from which you
can know if your Sfold run was successful. Most of the other
text files contain a header section that defines the formats
and meanings of the data in the output. For a comprehensive
description of the output files, please refer to our online
manual at:
http://www.wadsworth.org/resnres/bioinfo/sfold/manual.html
and the following papers about features on our Sfold Web
server:
- Ding, Y., Chan, C.Y. and Lawrence, C.E. (2004) Sfold web
server for statistical folding and rational design of
nucleic acids. Nucleic Acids Res. 32 Web Server issue,
W135-W141.
- Chan, C.Y., Lawrence, C.E. and Ding, Y. (2005) Structure
clustering features on the Sfold Web server.
Bioinformatics 21, 3926-3928.
============================================================
Last updated on June, 2017