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comparison SMART/Java/README.txt @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
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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. 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 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. 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 14
15 15
16 Instructions
17 ------------
18 Installation instructions and the user guide are available in the file "doc.pdf".
19
20
16 Copyright 21 Copyright
17 --------- 22 ---------
18 Copyright INRA-URGI 2009-2013 23 Copyright INRA-URGI 2009-2010
19 24
20 25
21 Authors 26 Authors
22 ------- 27 -------
23 Matthias Zytnicki 28 Matthias Zytnicki
33 This library is distributed under the terms of the CeCILL license 38 This library is distributed under the terms of the CeCILL license
34 (http://www.cecill.info/index.en.html). 39 (http://www.cecill.info/index.en.html).
35 See the LICENSE.txt file. 40 See the LICENSE.txt file.
36 41
37 42
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 43 Acknowledgements
68 ---------------- 44 ----------------
69 Many thanks go helping developers: 45 This product needs the following softwares :
70 - Yufei Luo 46 * R, under the GNU General Public License
71 - the URGI team 47 * MySQL, under the GNU General Public License
72 and the beta-testers: 48 * Python, under the Python License, compatible with the GNU General Public License
73 - Claire Toffano-Nioche 49 * MySQL for Python, under the GNU General Public License
74 - Claire Kuchly 50 * Java, under the GNU General Public License
75 - among others... 51