comparison SMART/Java/README.txt @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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1 ----------
2 | NAME |
3 ----------
4 S-MART
5
6
7 Description
8 -----------
9 Several tools are now available for mapping high-throughput sequencing data from a genome, but few can extract biological knowledge from the mapped reads. We have developed a toolbox, S-MART, which handles mapped RNA-Seq and ChIP-Seq data.
10
11 S-MART is an intuitive and lightweight tool, performing several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization.
12
13 S-MART does not require a computer science background and thus can be used by all biologists through a graphical interface. S-MART can run on any personal computer, yielding results within an hour for most queries.
14
15
16 Copyright
17 ---------
18 Copyright INRA-URGI 2009-2013
19
20
21 Authors
22 -------
23 Matthias Zytnicki
24
25
26 Contact
27 -------
28 urgi-contact@versailles.inra.fr
29
30
31 License
32 -------
33 This library is distributed under the terms of the CeCILL license
34 (http://www.cecill.info/index.en.html).
35 See the LICENSE.txt file.
36
37
38 Installation under Galaxy
39 -------------------------
40 S-MART is available under the Galaxy Tool Shed: http://toolshed.g2.bx.psu.edu/
41 Remember to set the variables "tool_config_file" and "tool_dependency_dir" accordingly. Please look up the Galaxy Tool Shed wiki to know more about it.
42 It assumes you have R installed, as well as two packages: RColorBrewer (for colors in graphics), and Hmisc (for statistics). You can install them as root with the commands:
43 - R --slave --no-save --no-restore --quiet -e 'if("RColorBrewer" %in% rownames(installed.packages()) == FALSE){install.packages("RColorBrewer", repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}'
44 - R --slave --no-save --no-restore --quiet -e 'if("Hmisc" %in% rownames(installed.packages()) == FALSE){install.packages("Hmisc", repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}'
45
46 Optionally, you can organize the layout of S-MART tools following these instructions. This way, all the tools will be correctly sorted and appear in categories.
47 - Locate the directory where S-MART has been installed: probably in "<galaxy install dir>/shed_tool/toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/XXX/s_mart/"
48 - Create a symbolic link "<galaxy install dir>/tools/s_mart" directing to "<S-MART install dir>/SMART/galaxy/"
49 - Paste the content of "<S-MART install dir>/SMART/galaxy/tool_conf.xml" to your local "<galaxy install dir>/tool_conf.xml", for instance, right before the </toolbox> mark-up.
50 - Remove the S-MART layout in "<galaxy install dir>/shed_tool_conf.xml" (the name may vary depending on your "universe_wgsi.ini" file) which has been automatically generated: remove the whole block between the markup <section id="s-mart" name="S-MART" version="XXX"> and the corresponding </section>.
51 - Restart Galaxy to complete the install.
52
53
54 Stand-alone installation
55 ------------------------
56 This product needs the following softwares :
57 - R, under the GNU General Public License, and several R package (under the same License)
58 - Python, under the Python License, compatible with the GNU General Public License
59 - Java, under the GNU General Public License
60
61
62 Instructions
63 ------------
64 Further installation instructions and the user guide are available in the file "doc.pdf".
65
66
67 Acknowledgements
68 ----------------
69 Many thanks go helping developers:
70 - Yufei Luo
71 - the URGI team
72 and the beta-testers:
73 - Claire Toffano-Nioche
74 - Claire Kuchly
75 - among others...