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annotate MANUAL_INSTALL.txt @ 1:301d7adf862e draft

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planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit df8740e6849320412c96468d3c99830b25b9f0d6
author lecorguille
date Mon, 04 Jul 2016 11:51:22 -0400
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a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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1 Instructions to integrate the "NMR bucketing" tool into a local instance of Galaxy
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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2 Version February 2015 M Tremblay-Franco
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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5 ## --- R bin and Packages : --- ##
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6 R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
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7 Platform: x86_64-redhat-linux-gnu (64-bit)
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9 Install the "batch" library, necessary for parseCommandArgs function and the "pracma" library, nessecary for cumtrapz function:
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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10 - Download package source (*.tar.gz file) from your favorite CRAN (http://www.r-project.org/)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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11 For example: http://cran.univ-lyon1.fr/
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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13 - Install package in your R session
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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14 install.packages("path/package_name.tar.gz",lib="path",repos=NULL)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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15 For Example: install.packages("/usr/lib64/R/library/pracma_1.8.3.tar",lib="/usr/lib64/R/library",repos=NULL)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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17 - Finally, load the package into your R session
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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18 library(batch)
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19 library(pracma)
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22 ## --- Config : --- ##
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23 - Edit the file "/galaxy/dist/galaxy-dist/tool_conf.xml" and add
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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24 <section id="id_name" name="Name">
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25 <tool file="path/NmrBucketing_xml.xml" />
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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26 </section>
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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27 to create a new section containing the NMR_Bucketing tool
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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28 or add
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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29 <tool file="path/NmrBucketing_xml.xml" />
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30 in an existing section
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a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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32 - Put the three files NmrBucketing_xml.xml, NmrBucketing_wrapper.R and NmrBucketing_script.R in a same directory
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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33 For example, path=/galaxy/dist/galaxy-dist/tools/stats
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35 - Edit the NmrBucketing_xml.xml file and change the path in the following lines
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36 # R script
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37 R --vanilla --slave --no-site-file --file=path/NmrBucketing_wrapper.R --args
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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39 ## Library name for raw files storage
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40 library path/$library
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42 ## --- XML help part --- ##
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43 one image:
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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44 Copy the 'Mth_Architecture_Repertoire_Bruker.png' file within the directory to your galaxy-dist/static/images/
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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:
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49 #In universe_wsgi.ini
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50 user_library_import_dir = /projet/sbr/galaxy/import/user
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52 #Create the user "myaccount" in this path
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54 User path: /projet/sbr/galaxy/import/user/myaccount@sb-roscoff.fr
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59 Finally, restart Galaxy