diff README.md @ 2:c8533e9298e5 draft

"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
author ppericard
date Fri, 23 Oct 2020 10:15:56 +0000
parents d0b77b926863
children
line wrap: on
line diff
--- a/README.md	Thu Oct 15 12:22:25 2020 +0000
+++ b/README.md	Fri Oct 23 10:15:56 2020 +0000
@@ -1,70 +1,33 @@
-# galaxy-mixomics-blocksplsda
-Galaxy wrappers for the block.splsda, plotIndiv and plotVar functions from the mixOmics R package
+# galaxy-viscorvar
+
+Galaxy wrappers for the visCorVar R package and selected functions from the mixOmics R package (block.splsda, plotIndiv and plotVar).
 
-# Install for developers
+## Install from Toolshed
+
+Install `viscorvar` repository from Galaxy ToolShed (owner: `ppericard`)
+
+## Install for developers
 
 Clone repository
 
 ```
-$ git clone --recurse-submodules https://gitlab.com/bilille/galaxy-mixomics-blocksplsda.git
+$ git clone --recurse-submodules https://gitlab.com/bilille/galaxy-viscorvar.git
 ```
 
-Add `galaxy-mixomics-blocksplsda` repository to `$GALAXYDIR/tools` directory.
+Add `galaxy-viscorvar` repository to `$GALAXYDIR/tools` directory.
 
 Edit `$GALAXYDIR/config/tool_conf.xml` and add:
 
 ```
 <section id="development" name="Tools development">
-  <label id="mixomics_blocksplsda" name="mixOmics blocksplsda" />
-    <tool file="galaxy-mixomics-blocksplsda/mixomics_blocksplsda.xml" />
-    <tool file="galaxy-mixomics-blocksplsda/mixomics_plotindiv.xml" />
-    <tool file="galaxy-mixomics-blocksplsda/mixomics_plotvar.xml" />
-    <tool file="galaxy-mixomics-blocksplsda/matCor_addVar.xml" />
-    <tool file="galaxy-mixomics-blocksplsda/computeMatSimilarity.xml" />
-    <tool file="galaxy-mixomics-blocksplsda/circleCor.xml" />
-    <tool file="galaxy-mixomics-blocksplsda/networkVar.xml" />
+  <label id="viscorvar" name="visCorVar" />
+    <tool file="galaxy-viscorvar/mixomics_blocksplsda.xml" />
+    <tool file="galaxy-viscorvar/mixomics_plotindiv.xml" />
+    <tool file="galaxy-viscorvar/mixomics_plotvar.xml" />
+    <tool file="galaxy-viscorvar/viscorvar_matcoraddvar.xml" />
+    <tool file="galaxy-viscorvar/viscorvar_circlecor.xml" />
+    <tool file="galaxy-viscorvar/viscorvar_computematsimilarity.xml" />
+    <tool file="galaxy-viscorvar/viscorvar_networkvar.xml" />
 </section>
 ```
 
-# Preparing Galaxy conda manual environment for visCorVar
-
-Activate Galaxy self-installed conda (for your shell; bash here) and reload terminal
-
-```
-$ . $GALAXYDIR/database/dependencies/_conda/bin/conda init bash
-```
-
-Create and activate conda environment for visCorVar package
-
-```
-$ conda create --name __viscorvar@0.1 && conda activate __viscorvar@0.1
-```
-
-Install dependencies
-
-```
-$ conda install bioconductor-mixomics r-rdpack r-igraph
-```
-
-Manually install visCorVar package from repository
-
-```
-$ R
-
-> install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.1.tar.gz", repos=NULL)
-> library(visCorVar)
-```
-
-
-
-
-
-
-
-
-
-
-
-
-
-