test

YuLab-SMU · Jan 3, 2017 · 6fe12e6 · 6fe12e6
1 parent 423a4ac
commit 6fe12e6
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Showing 15 changed files with 20 additions and 25 deletions.
diff --git a/.gitignore b/.gitignore
@@ -8,5 +8,3 @@ __init__.py
 __pycache__
 __init__.pyc
 
-mkdocs/mysoftware
-mkdocs/mysoftware
diff --git a/.gitmodules b/.gitmodules
diff --git a/Makefile b/Makefile
@@ -51,18 +51,18 @@ mkdocs: mdfiles
 	Rscript -e 'library(ypages); add_biobabble("index.html")'
 
 mysoftware:
-	git submodule add -f git@github.com:GuangchuangYu/mysoftware.git mkdocs/mysoftware
+	git submodule add -f git@github.com:GuangchuangYu/mysoftware.git mkdocs/mysoftware;\
+	rm -rf .gitmodules;\
+	rm -rf mkdocs/mysoftware/.git
 
 mdfiles:
 	cd mkdocs;\
-	rm -rf docs/*md;\
 	Rscript -e 'library(ypages); gendoc("src/index.md", "blue", "docs/index.md")';\
 	Rscript -e 'library(ypages); gendoc("src/documentation.md", "blue", "docs/documentation.md")';\
 	Rscript -e 'library(ypages); gendoc("src/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
 	Rscript -e 'library(ypages); gendoc("src/faq.md", "blue", "docs/faq.md")';\
 	cd docs;\
-	cp ../mysoftware/*.md ./
-
+	ln -f -s ../mysoftware/* ./
 
 svnignore:
 	svn propset svn:ignore -F .svnignore .

diff --git a/docs/featuredArticles/index.html b/docs/featuredArticles/index.html
@@ -223,11 +223,11 @@
   }  
   </style>
 
-<div id = 'chart3cdd731534da' class = 'rChart morris'></div>
+<div id = 'chart3e0e14505d80' class = 'rChart morris'></div>
 
 <script type='text/javascript'>
     var chartParams = {
- "element": "chart3cdd731534da",
+ "element": "chart3e0e14505d80",
 "width":            800,
 "height":            400,
 "xkey": "year",
@@ -241,7 +241,7 @@
 "pubid": "HtEfBTGE9r8C" 
 } 
 ],
-"id": "chart3cdd731534da",
+"id": "chart3e0e14505d80",
 "labels": "cites" 
 },
       chartType = "Bar"

diff --git a/docs/mkdocs/search_index.json b/docs/mkdocs/search_index.json
@@ -207,7 +207,7 @@
         }, 
         {
             "location": "/featuredArticles/", 
-            "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", 
+            "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", 
             "title": "Featured Articles"
         }, 
         {

diff --git a/mkdocs/docs/ChIPseeker.md b/mkdocs/docs/ChIPseeker.md
diff --git a/mkdocs/docs/ChIPseeker.md b/mkdocs/docs/ChIPseeker.md
@@ -0,0 +1 @@
+../mysoftware/ChIPseeker.md
diff --git a/mkdocs/docs/DOSE.md b/mkdocs/docs/DOSE.md
diff --git a/mkdocs/docs/DOSE.md b/mkdocs/docs/DOSE.md
@@ -0,0 +1 @@
+../mysoftware/DOSE.md
diff --git a/mkdocs/docs/GOSemSim.md b/mkdocs/docs/GOSemSim.md
diff --git a/mkdocs/docs/GOSemSim.md b/mkdocs/docs/GOSemSim.md
@@ -0,0 +1 @@
+../mysoftware/GOSemSim.md
diff --git a/mkdocs/docs/ReactomePA.md b/mkdocs/docs/ReactomePA.md
diff --git a/mkdocs/docs/ReactomePA.md b/mkdocs/docs/ReactomePA.md
@@ -0,0 +1 @@
+../mysoftware/ReactomePA.md
diff --git a/mkdocs/docs/clusterProfiler.md b/mkdocs/docs/clusterProfiler.md
diff --git a/mkdocs/docs/clusterProfiler.md b/mkdocs/docs/clusterProfiler.md
@@ -0,0 +1 @@
+../mysoftware/clusterProfiler.md
diff --git a/mkdocs/docs/emojifont.md b/mkdocs/docs/emojifont.md
diff --git a/mkdocs/docs/emojifont.md b/mkdocs/docs/emojifont.md
@@ -0,0 +1 @@
+../mysoftware/emojifont.md
diff --git a/mkdocs/docs/featuredArticles.md b/mkdocs/docs/featuredArticles.md
@@ -36,10 +36,10 @@
   }  
   </style>
 
-<div id = 'chart3cdd731534da' class = 'rChart morris'></div>
+<div id = 'chart3e0e14505d80' class = 'rChart morris'></div>
 <script type='text/javascript'>
     var chartParams = {
- "element": "chart3cdd731534da",
+ "element": "chart3e0e14505d80",
 "width":            800,
 "height":            400,
 "xkey": "year",
@@ -53,7 +53,7 @@
 "pubid": "HtEfBTGE9r8C" 
 } 
 ],
-"id": "chart3cdd731534da",
+"id": "chart3e0e14505d80",
 "labels": "cites" 
 },
       chartType = "Bar"

diff --git a/mkdocs/docs/ggtree.md b/mkdocs/docs/ggtree.md
diff --git a/mkdocs/docs/ggtree.md b/mkdocs/docs/ggtree.md
@@ -0,0 +1 @@
+../mysoftware/ggtree.md
diff --git a/mkdocs/docs/meshes.md b/mkdocs/docs/meshes.md
diff --git a/mkdocs/docs/meshes.md b/mkdocs/docs/meshes.md
@@ -0,0 +1 @@
+../mysoftware/meshes.md
diff --git a/mkdocs/docs/treeio.md b/mkdocs/docs/treeio.md
diff --git a/mkdocs/docs/treeio.md b/mkdocs/docs/treeio.md
@@ -0,0 +1 @@
+../mysoftware/treeio.md