Mercurial > repos > matces > carpet_toolsuite

diff carpet-src-1/INSTALL @ 0:cdd489d98766
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author: matces
date: Tue, 07 Jun 2011 16:50:41 -0400
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/carpet-src-1/INSTALL	Tue Jun 07 16:50:41 2011 -0400
@@ -0,0 +1,39 @@
+Prerequisites:
+- a working installation of galaxy
+- R/Bioconductor
+- Ringo bioconductor library
+- rpy (version 1.0.x)
+- a working C++ compiler
+
+Installation:
+given a galaxy dir $GALAXYTOPDIR
+- extract the content of the archive into $GALAXYTOPDIR:
+
+  tar cvjf carpet.tar.bz2 -C $GALAXYTOPDIR
+  
+- build the "comuni" executable:
+  
+  cd $GALAXYTOPDIR/tools/CARPET
+  g++ com_uni.cpp -o comuni
+  
+  (do NOT use optimizations if possible)
+  
+- paste the content of add_to_tool_conf.xml within tool_conf.xml 
+file (part of galaxy distribution), where needed and between the
+<toolbox></toolbox> tags
+
+- restart galaxy
+
+NOTES:
+- rpy2 is not implemented in carpet yet. You can download rpy (1.0.3) here:
+
+http://sourceforge.net/projects/rpy/files/rpy/1.0.3/rpy-1.0.3.tar.gz/download
+
+- You may install bioconductor's Ringo library just issuing the following within
+your R console:
+
+  source("http://bioconductor.org/biocLite.R")
+  biocLite("Ringo")
+  
+- carpet has been deployed and tested on galaxy build 1349. There's no warranty it 
+works on different builds (although it should).
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