From 5e7fed84d3d94dbd0134c0cc2db04d0454545246 Mon Sep 17 00:00:00 2001 From: Shraddha Pai Date: Thu, 31 Aug 2017 18:02:39 -0400 Subject: [PATCH] Update README.md --- README.md | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 917e282c..0c622bcb 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,7 @@ You must have Java, Python and R installed. Within R, you must have BioConductor of these you need to install. If you already have all these, skip to the next section. #### Java (1.8+ recommended, but will probably work on 1.6+) -netDx uses the GeneMANIA algorithm to integrate patient networks and recommend patients by similarity (Mostafavi and Morris (2008). *Genome Biol* 9:Suppl 1). GeneMANIA is currently implemented in Java, making this interpreter a requirement for netDx. +netDx uses the GeneMANIA algorithm to integrate patient networks and recommend patients by similarity (Mostafavi and Morris (2008). *Genome Biol* 9:Suppl 1). GeneMANIA is currently implemented in Java, making this interpreter a requirement for netDx. At command line, run `java --version`. You should see output like this: ``` @@ -78,7 +78,9 @@ This section assumes you have Java, Python, R and Bioconductor installed. From c ``` $ cd netDx-master/ $ R -> install.packages(c("bigmemory","foreach","combinat","doParallel","ROCR","pracma","RColorBrewer","reshape2","igraph")) +> install.packages(c('devtools','curl')) +> install.packages(c("bigmemory","foreach","combinat","doParallel","ROCR","pracma","RColorBrewer","reshape2")) +> devtools::install_github("igraph/rigraph") # install from CRAN has a bug and can fail (31 Aug 2017). > install.packages("netDx",type="source",repos=NULL) > install.packages("netDx.examples",type="source",repos=NULL) > install.packages("knitr") # needed to run examples @@ -89,17 +91,19 @@ Run the medulloblastoma vignette to make sure the netDx pipeline works from end Each vignette is in Sweave format (`.Rnw`) . To run these, you need to have both `netDx` and `netDx.examples` installed. You will also need to install the R package `knitr` to compile the Sweave file. If you have [Rstudio](https://www.rstudio.com/home/) installed (highly recommended), you should be able to open the `Rnw` file and click `Compile PDF`. Alternately, you may run the vignette through an interactive R session: ``` -$ cd netDx/examples/ +$ cd netDx-master/examples/ $ R > require(knitr) > knit2pdf("Medulloblastoma.Rnw") ``` -This should generate `Medulloblastoma.pdf` in the `examples/` directory. +This should generate `Medulloblastoma.pdf` in the `examples/` directory. ## Known issues with compiling pdfs -#### (Linux) -If you are getting an error saying that R cannot find `/usr/bin/texti2dvi`, install the `texinfo` package. +#### (Linux) +If you are getting an error saying that R cannot find `/usr/bin/texti2dvi`, install the `texinfo` and 'texlive' packages in linux. You can use the commands: +apt-get install texinfo +apt-get install texlive #### (OS/X): "`pdfLaTex` not found" error When compiling the pdf, you may get a message saying that `pdfLaTex` is not installed. We have had one such report on OS/X and it is known to occur after an upgrade to OS X Mavericks. The following steps resolved the issue (paraphrased from [this post](http://stackoverflow.com/questions/22081991/rmarkdown-pandoc-pdflatex-not-found)):