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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 1eda261d4fe137d6e8806b0c6af7eaf12d11ac95"
author ppericard
date Thu, 15 Oct 2020 12:22:25 +0000
parents d0b77b926863
children c8533e9298e5
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1 # galaxy-mixomics-blocksplsda
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2 Galaxy wrappers for the block.splsda, plotIndiv and plotVar functions from the mixOmics R package
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4 # Install for developers
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6 Clone repository
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8 ```
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9 $ git clone --recurse-submodules https://gitlab.com/bilille/galaxy-mixomics-blocksplsda.git
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10 ```
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12 Add `galaxy-mixomics-blocksplsda` repository to `$GALAXYDIR/tools` directory.
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14 Edit `$GALAXYDIR/config/tool_conf.xml` and add:
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16 ```
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17 <section id="development" name="Tools development">
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18 <label id="mixomics_blocksplsda" name="mixOmics blocksplsda" />
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19 <tool file="galaxy-mixomics-blocksplsda/mixomics_blocksplsda.xml" />
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20 <tool file="galaxy-mixomics-blocksplsda/mixomics_plotindiv.xml" />
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21 <tool file="galaxy-mixomics-blocksplsda/mixomics_plotvar.xml" />
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22 <tool file="galaxy-mixomics-blocksplsda/matCor_addVar.xml" />
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23 <tool file="galaxy-mixomics-blocksplsda/computeMatSimilarity.xml" />
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24 <tool file="galaxy-mixomics-blocksplsda/circleCor.xml" />
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25 <tool file="galaxy-mixomics-blocksplsda/networkVar.xml" />
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26 </section>
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27 ```
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29 # Preparing Galaxy conda manual environment for visCorVar
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31 Activate Galaxy self-installed conda (for your shell; bash here) and reload terminal
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33 ```
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34 $ . $GALAXYDIR/database/dependencies/_conda/bin/conda init bash
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35 ```
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37 Create and activate conda environment for visCorVar package
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39 ```
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40 $ conda create --name __viscorvar@0.1 && conda activate __viscorvar@0.1
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41 ```
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43 Install dependencies
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45 ```
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46 $ conda install bioconductor-mixomics r-rdpack r-igraph
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47 ```
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49 Manually install visCorVar package from repository
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51 ```
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52 $ R
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54 > install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.1.tar.gz", repos=NULL)
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55 > library(visCorVar)
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56 ```
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