|
0
|
1 Galaxy wrapper using R and RPy2
|
|
|
2 ===============================
|
|
|
3
|
|
|
4 These wrappers are based on RPy1 versions included in Galaxy-Main and
|
|
|
5 ported by John Chilton to RPy2. Please see the following Mail from
|
|
|
6 galaxy-dev:
|
|
|
7
|
|
|
8 http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014694.html
|
|
|
9
|
|
|
10 Missing ports to RPy2:
|
|
|
11
|
|
|
12 - rgenetics/rgQC.py
|
|
|
13 - regVariation/rcve.py
|
|
|
14 - ngs_simulation/ngs_simulation.py
|
|
|
15 - metag_tools/short_reads_figure_high_quality_length.py
|
|
|
16 - taxonomy/poisson2test.py
|
|
|
17
|
|
|
18 ToDo:
|
|
|
19
|
|
|
20 - add tool_dependencies.xml to RPy2 and R-3.0
|
|
|
21 - testing
|
|
|
22 - porting of missing tools
|
|
|
23
|
|
|
24
|
|
|
25 ============
|
|
|
26 Installation
|
|
|
27 ============
|
|
|
28
|
|
|
29
|
|
|
30
|
|
|
31 =======
|
|
|
32 History
|
|
|
33 =======
|
|
|
34
|
|
|
35
|
|
|
36 - v0.1: no release yet
|
|
|
37
|
|
|
38
|
|
|
39
|
|
|
40
|
|
|
41 Wrapper Licence (MIT/BSD style)
|
|
|
42 ===============================
|
|
|
43
|
|
|
44 Permission to use, copy, modify, and distribute this software and its
|
|
|
45 documentation with or without modifications and for any purpose and
|
|
|
46 without fee is hereby granted, provided that any copyright notices
|
|
|
47 appear in all copies and that both those copyright notices and this
|
|
|
48 permission notice appear in supporting documentation, and that the
|
|
|
49 names of the contributors or copyright holders not be used in
|
|
|
50 advertising or publicity pertaining to distribution of the software
|
|
|
51 without specific prior permission.
|
|
|
52
|
|
|
53 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
|
|
|
54 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
|
|
|
55 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
|
|
|
56 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
|
|
|
57 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
|
|
|
58 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
|
|
|
59 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
|
|
|
60 OR PERFORMANCE OF THIS SOFTWARE.
|
|
|
61
|
