guangchuang yu authored on 03/01/2017 10:03:26
Showing24 changed files

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@@ -8,5 +8,3 @@ __init__.py
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 __pycache__
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 __init__.pyc
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-mkdocs/mysoftware
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-mkdocs/mysoftware
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deleted file mode 100644
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@@ -1,3 +0,0 @@
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-[submodule "mkdocs/mysoftware"]
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-	path = mkdocs/mysoftware
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-	url = git@github.com:GuangchuangYu/mysoftware.git
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@@ -51,18 +51,18 @@ mkdocs: mdfiles
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 	Rscript -e 'library(ypages); add_biobabble("index.html")'
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 mysoftware:
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-	git submodule add -f git@github.com:GuangchuangYu/mysoftware.git mkdocs/mysoftware
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+	git submodule add -f git@github.com:GuangchuangYu/mysoftware.git mkdocs/mysoftware;\
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+	rm -rf .gitmodules;\
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+	rm -rf mkdocs/mysoftware/.git
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 mdfiles:
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 	cd mkdocs;\
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-	rm -rf docs/*md;\
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 	Rscript -e 'library(ypages); gendoc("src/index.md", "blue", "docs/index.md")';\
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 	Rscript -e 'library(ypages); gendoc("src/documentation.md", "blue", "docs/documentation.md")';\
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 	Rscript -e 'library(ypages); gendoc("src/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
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 	Rscript -e 'library(ypages); gendoc("src/faq.md", "blue", "docs/faq.md")';\
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 	cd docs;\
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-	cp ../mysoftware/*.md ./
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-
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+	ln -f -s ../mysoftware/* ./
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 svnignore:
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 	svn propset svn:ignore -F .svnignore .
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@@ -223,11 +223,11 @@
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   }  
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   </style>
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-<div id = 'chart3cdd731534da' class = 'rChart morris'></div>
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+<div id = 'chart3e0e14505d80' class = 'rChart morris'></div>
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 <script type='text/javascript'>
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     var chartParams = {
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- "element": "chart3cdd731534da",
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+ "element": "chart3e0e14505d80",
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 "width":            800,
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 "height":            400,
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 "xkey": "year",
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@@ -241,7 +241,7 @@
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 "pubid": "HtEfBTGE9r8C" 
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 } 
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 ],
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-"id": "chart3cdd731534da",
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+"id": "chart3e0e14505d80",
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 "labels": "cites" 
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 },
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       chartType = "Bar"
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@@ -207,7 +207,7 @@
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         }, 
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         {
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             "location": "/featuredArticles/", 
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-            "text": "Let us know\n if you have published using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }  \n  \n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart3cdd731534da\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart3cdd731534da\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape\n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens\n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015\n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species\n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976", 
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+            "text": "Let us know\n if you have published using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }  \n  \n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart3e0e14505d80\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart3e0e14505d80\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape\n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens\n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015\n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species\n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976", 
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             "title": "Featured Articles"
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         }, 
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         {
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-<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/ChIPseeker" />
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new file mode 120000
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+../mysoftware/ChIPseeker.md
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\ No newline at end of file
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-<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/DOSE" />
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+../mysoftware/DOSE.md
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\ No newline at end of file
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-<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/GOSemSim" />
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new file mode 120000
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+../mysoftware/GOSemSim.md
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\ No newline at end of file
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-<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/ReactomePA" />
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+../mysoftware/ReactomePA.md
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\ No newline at end of file
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-<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/clusterProfiler" />
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+../mysoftware/clusterProfiler.md
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\ No newline at end of file
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-<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/emojifont" />
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+../mysoftware/emojifont.md
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\ No newline at end of file
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@@ -36,10 +36,10 @@
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   }  
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   </style>
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-<div id = 'chart3cdd731534da' class = 'rChart morris'></div>
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+<div id = 'chart3e0e14505d80' class = 'rChart morris'></div>
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 <script type='text/javascript'>
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     var chartParams = {
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- "element": "chart3cdd731534da",
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+ "element": "chart3e0e14505d80",
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 "width":            800,
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 "height":            400,
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 "xkey": "year",
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@@ -53,7 +53,7 @@
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 "pubid": "HtEfBTGE9r8C" 
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 } 
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 ],
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-"id": "chart3cdd731534da",
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+"id": "chart3e0e14505d80",
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 "labels": "cites" 
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 },
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       chartType = "Bar"
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deleted file mode 100644
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-<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/ggtree" />
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+../mysoftware/ggtree.md
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-<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/meshes" />
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+../mysoftware/meshes.md
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\ No newline at end of file
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-<meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/treeio" />
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+../mysoftware/treeio.md
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\ No newline at end of file