Skip to content

Adding dependency details to README.md #20

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
rfara wants to merge 3 commits into
base: dev
Choose a base branch
from
Open

Adding dependency details to README.md #20

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
768ea01
Adding dependency details to README.md
rfara Sep 14, 2023
d2c2711
Update README.md
rfara Sep 14, 2023
41e0db8
Update README.md
rfara Sep 14, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 13 additions & 3 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
```
Expand All @@ -49,12 +51,16 @@ You can then activate the environment using:
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 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
Expand All @@ -69,6 +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:
Expand All @@ -79,6 +87,8 @@ 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
Expand Down