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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
author ppericard
date Tue, 23 Jun 2020 19:57:35 -0400
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1 # galaxy-mixomics-blocksplsda
2 Galaxy wrappers for the block.splsda, plotIndiv and plotVar functions from the mixOmics R package
3
4 # Install for developers
5
6 Clone repository
7
8 ```
9 $ git clone --recurse-submodules https://gitlab.com/bilille/galaxy-mixomics-blocksplsda.git
10 ```
11
12 Add `galaxy-mixomics-blocksplsda` repository to `$GALAXYDIR/tools` directory.
13
14 Edit `$GALAXYDIR/config/tool_conf.xml` and add:
15
16 ```
17 <section id="development" name="Tools development">
18 <label id="mixomics_blocksplsda" name="mixOmics blocksplsda" />
19 <tool file="galaxy-mixomics-blocksplsda/mixomics_blocksplsda.xml" />
20 <tool file="galaxy-mixomics-blocksplsda/mixomics_plotindiv.xml" />
21 <tool file="galaxy-mixomics-blocksplsda/mixomics_plotvar.xml" />
22 <tool file="galaxy-mixomics-blocksplsda/matCor_addVar.xml" />
23 <tool file="galaxy-mixomics-blocksplsda/computeMatSimilarity.xml" />
24 <tool file="galaxy-mixomics-blocksplsda/circleCor.xml" />
25 <tool file="galaxy-mixomics-blocksplsda/networkVar.xml" />
26 </section>
27 ```
28
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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