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comparison MANUAL_INSTALL.txt @ 3:966fcf7ae66e draft

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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 9ca88a22e9b9394bfa00ea383fbb2b78ef05f990
author lecorguille
date Thu, 26 Oct 2017 06:01:14 -0400
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2:3cd762aac7a4 3:966fcf7ae66e
1 Instructions to integrate the NMR Normalization" tool into a local instance of Galaxy
2 Version mars 2015 M Tremblay-Franco
3
4
5 ## --- R bin and Packages : --- ##
6 R version 3.0.2 (2013-09-25) -- "Frisbee Sailing
7 Platform: x86_64-redhat-linux-gnu (64-bit)
8
9 Install the "batch" library, necessary for parseCommandArgs function:
10 - Download package source (*.tar.gz file) from your favorite CRAN (http://www.r-project.org/)
11 For example: http://cran.univ-lyon1.fr/
12
13 - Install package in your R session
14 install.packages("path/package_name.tar.gz",lib="path",repos=NULL)
15 For Example: install.packages("/usr/lib64/R/library/batch_1.1-4.tar",lib="/usr/lib64/R/library",repos=NULL)
16
17 - Finally, load the package into your R session
18 library(batch)
19
20
21
22 ## --- Config : --- ##
23 - Edit the file "/galaxy/dist/galaxy-dist/tool_conf.xml" and add
24 <section id="id_name" name="Name">
25 <tool file="path/NmrNormalization_xml.xml" />
26 </section>
27 to create a new section containing the Nmr_Normalization tool
28 or add
29 <tool file="path/NmrNormalization_xml.xml" />
30 in an existing section
31
32 - Put the three files NmrNormalization_xml.xml, NmrNormalization_wrapper.R and NmrNormalization_script.R in a same directory
33 For example, path=/galaxy/dist/galaxy-dist/tools/stats
34
35 - Edit the NmrBucketing_xml.xml file and change the path in the following lines
36 # R script
37 R --vanilla --slave --no-site-file --file=path/NmrNormalization_wrapper.R --args
38
39 ## Library name for raw files storage
40 library path/$library
41
42
43
44 Finally, restart Galaxy