diff nmr_bucketing/MANUAL_INSTALL.txt @ 2:3cd762aac7a4 draft

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+Instructions to integrate the "NMR bucketing" tool into a local instance of Galaxy
+Version February 2015 M Tremblay-Franco
+
+
+## --- R bin and Packages : --- ##
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+Platform: x86_64-redhat-linux-gnu (64-bit)
+
+Install the "batch" library, necessary for parseCommandArgs function and the "pracma" library, nessecary for cumtrapz function:
+ - Download package source (*.tar.gz file) from your favorite CRAN (http://www.r-project.org/)
+For example: http://cran.univ-lyon1.fr/
+
+ - Install package in your R session
+install.packages("path/package_name.tar.gz",lib="path",repos=NULL)
+For Example: install.packages("/usr/lib64/R/library/pracma_1.8.3.tar",lib="/usr/lib64/R/library",repos=NULL)
+
+ - Finally, load the package into your R session
+library(batch)
+library(pracma)
+
+
+## --- Config : --- ##
+ - Edit the file "/galaxy/dist/galaxy-dist/tool_conf.xml" and add 
+<section id="id_name" name="Name">
+  <tool file="path/NmrBucketing_xml.xml" />
+</section>
+to create a new section containing the NMR_Bucketing tool
+or add
+  <tool file="path/NmrBucketing_xml.xml" />
+in an existing section
+
+ - Put the three files NmrBucketing_xml.xml, NmrBucketing_wrapper.R and NmrBucketing_script.R in a same directory
+For example, path=/galaxy/dist/galaxy-dist/tools/stats
+
+ - Edit the NmrBucketing_xml.xml file and change the path in the following lines
+    # R script
+    R --vanilla --slave --no-site-file --file=path/NmrBucketing_wrapper.R --args
+    
+    ## Library name for raw files storage
+    library path/$library
+
+## --- XML help part --- ##
+one image: 
+Copy the 'Mth_Architecture_Repertoire_Bruker.png' file within the directory to your galaxy-dist/static/images/
+
+
+ - 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:
+
+	#In universe_wsgi.ini
+ 		user_library_import_dir = /projet/sbr/galaxy/import/user
+
+	#Create the user "myaccount" in this path
+
+		User path: /projet/sbr/galaxy/import/user/[e-mail]
+
+
+
+
+Finally, restart Galaxy
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