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comparison MANUAL_INSTALL.txt @ 0:a99a6026c972 draft

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planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
author marie-tremblay-metatoul
date Fri, 08 Apr 2016 10:56:14 -0400
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1 Instructions to integrate the "NMR bucketing" tool into a local instance of Galaxy
2 Version February 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 and the "pracma" library, nessecary for cumtrapz 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/pracma_1.8.3.tar",lib="/usr/lib64/R/library",repos=NULL)
16
17 - Finally, load the package into your R session
18 library(batch)
19 library(pracma)
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/NmrBucketing_xml.xml" />
26 </section>
27 to create a new section containing the NMR_Bucketing tool
28 or add
29 <tool file="path/NmrBucketing_xml.xml" />
30 in an existing section
31
32 - Put the three files NmrBucketing_xml.xml, NmrBucketing_wrapper.R and NmrBucketing_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/NmrBucketing_wrapper.R --args
38
39 ## Library name for raw files storage
40 library path/$library
41
42 ## --- XML help part --- ##
43 one image:
44 Copy the 'Mth_Architecture_Repertoire_Bruker.png' file within the directory to your galaxy-dist/static/images/
45
46
47 - Activate the "user_library_import_dir" in your /galaxy/dist/galaxy-dist/universe_wsgi.ini and create the users directories in this path, for example:
48
49 #In universe_wsgi.ini
50 user_library_import_dir = /projet/sbr/galaxy/import/user
51
52 #Create the user "myaccount" in this path
53
54 User path: /projet/sbr/galaxy/import/user/myaccount@sb-roscoff.fr
55
56
57
58
59 Finally, restart Galaxy