From 768ea01c8bb43333d3276c85f7e1df18c0e5d3e6 Mon Sep 17 00:00:00 2001 From: Rupert <42964280+rfara@users.noreply.github.com> Date: Thu, 14 Sep 2023 15:18:55 +0300 Subject: [PATCH 1/3] Adding dependency details to README.md --- README.md | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index e76e7de..53ce803 100644 --- a/README.md +++ b/README.md @@ -29,7 +29,9 @@ For more details please see the _Methods_ section of the manuscript. ## Installation -To install GeRM, first clone the repository to your local computer with +Installation has been tested using Mac OS Ventura 13.5.2 and CentOS Linux 7 Core. GeRM requires only a standard desktop computer or laptop, but the RAM requirements will scale with the lenth of the input sequences. + +To install GeRM, first clone the repository to your local computer with: ``` git clone https://github.com/ulelab/germ.git ``` @@ -49,9 +51,11 @@ You can then activate the environment using: conda activate germs ``` +The environment should take approximately 10 minutes to build. + ### 2. R option -GeRM requires R to be installed on your system and uses some R (`optparse`, `devtools`, `data.table`, `tidyverse`, `scales`, `ggthemes`, `cowplot`, `patchwork`, `logger`) and Bioconductor packages (`Biostrings`). If you have R already installed, you can install the GeRM R package by moving to the directory into which you cloned GeRM and then run: +GeRM requires R to be installed on your system (tested with R 4.1.2 and 4.2.0) and uses some R (`optparse`, `devtools`, `data.table`, `tidyverse`, `scales`, `ggthemes`, `cowplot`, `patchwork`, `logger`) and Bioconductor packages (`Biostrings`). If you have R already installed, you can install the GeRM R package by moving to the directory into which you cloned GeRM and then run: ``` R -e 'devtools:install()' From d2c2711d71199dd74ab90af7ebc9ea4c00ec8c43 Mon Sep 17 00:00:00 2001 From: Rupert <42964280+rfara@users.noreply.github.com> Date: Thu, 14 Sep 2023 16:50:48 +0300 Subject: [PATCH 2/3] Update README.md --- README.md | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 53ce803..c426b5c 100644 --- a/README.md +++ b/README.md @@ -53,12 +53,14 @@ conda activate germs The environment should take approximately 10 minutes to build. +>Note: the environment creation has failed in one case due to old GCC compiler versions (<= 11) being pointed to in the R Makefile. If you receive error messages such as `g++-11: warning: could not understand version 13.05.00`, you may need to update your Makefile paths to point to a more recent compiler (e.g. GCC 12). + ### 2. R option -GeRM requires R to be installed on your system (tested with R 4.1.2 and 4.2.0) and uses some R (`optparse`, `devtools`, `data.table`, `tidyverse`, `scales`, `ggthemes`, `cowplot`, `patchwork`, `logger`) and Bioconductor packages (`Biostrings`). If you have R already installed, you can install the GeRM R package by moving to the directory into which you cloned GeRM and then run: +GeRM requires R to be installed on your system (tested with R 4.1.2 and 4.2.0) and uses some R (`optparse`, `devtools`, `data.table`, `tidyverse`, `scales`, `ggthemes`, `cowplot`, `patchwork`, `logger`) and Bioconductor packages (`Biostrings`). If you have already installed R and these dependencies, you can install the GeRM R package by moving to the directory into which you cloned GeRM and then run: ``` -R -e 'devtools:install()' +R -e 'devtools::install()' ``` ### 3. Docker option @@ -83,6 +85,8 @@ Rscript germs.R --help This will output the help for all the parameters that can be supplied to GeRM. The minimum is to provide a FASTA file with sequences for which to calculate GeRM scores (`--fasta`, `-f`) +The germs.R file also serves of an example of how you can implement GeRM in to your own R scripts. + ## Parameters ### Basic From 41e0db873dc25bd80704d3b9f95fe0b5b32503a2 Mon Sep 17 00:00:00 2001 From: Rupert <42964280+rfara@users.noreply.github.com> Date: Thu, 14 Sep 2023 16:59:07 +0300 Subject: [PATCH 3/3] Update README.md --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index c426b5c..23cf1b2 100644 --- a/README.md +++ b/README.md @@ -75,6 +75,8 @@ To test the installation has worked you can run the test script. This runs three bash testrun.sh ``` +The test script should take 1-2 minutes to run, and should output test plots (in the `plots` and `plots_nonstdchars` directories) as well as a sample table of k-mer multivalencies (`test_5_123_123.multivalency.tsv.gz` and `output_nonstdchars.tsv.gz` in the working directory). + ## Quickstart GeRM can be run from the command line using: