Mercurial > repos > ppericard > viscorvar
diff README.md @ 2:c8533e9298e5 draft
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
author | ppericard |
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date | Fri, 23 Oct 2020 10:15:56 +0000 |
parents | d0b77b926863 |
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--- 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) -``` - - - - - - - - - - - - - -