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"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
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1:e93350dc99f1 2:c8533e9298e5
1 # galaxy-mixomics-blocksplsda 1 # galaxy-viscorvar
2 Galaxy wrappers for the block.splsda, plotIndiv and plotVar functions from the mixOmics R package
3 2
4 # Install for developers 3 Galaxy wrappers for the visCorVar R package and selected functions from the mixOmics R package (block.splsda, plotIndiv and plotVar).
4
5 ## Install from Toolshed
6
7 Install `viscorvar` repository from Galaxy ToolShed (owner: `ppericard`)
8
9 ## Install for developers
5 10
6 Clone repository 11 Clone repository
7 12
8 ``` 13 ```
9 $ git clone --recurse-submodules https://gitlab.com/bilille/galaxy-mixomics-blocksplsda.git 14 $ git clone --recurse-submodules https://gitlab.com/bilille/galaxy-viscorvar.git
10 ``` 15 ```
11 16
12 Add `galaxy-mixomics-blocksplsda` repository to `$GALAXYDIR/tools` directory. 17 Add `galaxy-viscorvar` repository to `$GALAXYDIR/tools` directory.
13 18
14 Edit `$GALAXYDIR/config/tool_conf.xml` and add: 19 Edit `$GALAXYDIR/config/tool_conf.xml` and add:
15 20
16 ``` 21 ```
17 <section id="development" name="Tools development"> 22 <section id="development" name="Tools development">
18 <label id="mixomics_blocksplsda" name="mixOmics blocksplsda" /> 23 <label id="viscorvar" name="visCorVar" />
19 <tool file="galaxy-mixomics-blocksplsda/mixomics_blocksplsda.xml" /> 24 <tool file="galaxy-viscorvar/mixomics_blocksplsda.xml" />
20 <tool file="galaxy-mixomics-blocksplsda/mixomics_plotindiv.xml" /> 25 <tool file="galaxy-viscorvar/mixomics_plotindiv.xml" />
21 <tool file="galaxy-mixomics-blocksplsda/mixomics_plotvar.xml" /> 26 <tool file="galaxy-viscorvar/mixomics_plotvar.xml" />
22 <tool file="galaxy-mixomics-blocksplsda/matCor_addVar.xml" /> 27 <tool file="galaxy-viscorvar/viscorvar_matcoraddvar.xml" />
23 <tool file="galaxy-mixomics-blocksplsda/computeMatSimilarity.xml" /> 28 <tool file="galaxy-viscorvar/viscorvar_circlecor.xml" />
24 <tool file="galaxy-mixomics-blocksplsda/circleCor.xml" /> 29 <tool file="galaxy-viscorvar/viscorvar_computematsimilarity.xml" />
25 <tool file="galaxy-mixomics-blocksplsda/networkVar.xml" /> 30 <tool file="galaxy-viscorvar/viscorvar_networkvar.xml" />
26 </section> 31 </section>
27 ``` 32 ```
28 33
29 # Preparing Galaxy conda manual environment for visCorVar
30
31 Activate Galaxy self-installed conda (for your shell; bash here) and reload terminal
32
33 ```
34 $ . $GALAXYDIR/database/dependencies/_conda/bin/conda init bash
35 ```
36
37 Create and activate conda environment for visCorVar package
38
39 ```
40 $ conda create --name __viscorvar@0.1 && conda activate __viscorvar@0.1
41 ```
42
43 Install dependencies
44
45 ```
46 $ conda install bioconductor-mixomics r-rdpack r-igraph
47 ```
48
49 Manually install visCorVar package from repository
50
51 ```
52 $ R
53
54 > install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.1.tar.gz", repos=NULL)
55 > library(visCorVar)
56 ```
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