Commit d4838a93 authored by Rebecca E Batorsky's avatar Rebecca E Batorsky
Browse files

Installation Instructions

parent e3890a70
......@@ -5,19 +5,21 @@ This is a repository to work on the error prone dna repair project with the McVe
**Installation**
Installation via Miniconda3 is recommended:
- Configure on the command line to use GitLab on the command line
`git config --global user.name "tufts username"` (Tufts username is usually 5 letters followed by 2 numbers)
`git config --global user.email "first.last@tufts.edu"`
- Configure on the command line to use GitLab on the command line
`git config --global user.name "tufts username"` (Tufts username is usually 5 letters followed by 2 numbers)
`git config --global user.email "first.last@tufts.edu"`
- Download repository
- Download repository (you will be prompted for password)
`git clone https://gitlab.tufts.edu/rbator01/sdmmej.git`
You will be prompted for password.
Note that you can also download the repository from the web browser if there are problems configuring command line git access.
- Download and install Miniconda3, the following will work on Mac OS
- Download and install Miniconda3, the following will work on Mac OS
`curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh --output Miniconda3-latest-MacOSX-x86_64.sh`
`bash Miniconda3-latest-MacOSX-x86_64.sh`
follow prompts to accept license and run "conda init" on startup
follow prompts to accept license and "yes" to running "conda init" on startup
`source ~/.bash_profile`
- Create Conda environment
......@@ -27,9 +29,10 @@ follow prompts to accept license and run "conda init" on startup
`conda create -n sdmmej  r-base=4.0.3 r-dplyr r-stringr bioconductor-biostrings python=2.7 pandas`
- To activate and deactivate you will use
- To activate and deactivate you will use
`conda activate sdmmej`
`conda deactivate sdmmej`
**Pipeline Script**
This script takes the path to the HiFibr output file as the single command line argument.
......@@ -37,11 +40,11 @@ Other default arguments are set within the script.
Example usage on test data:
`conda activate sdmmej`
`cd sdmmej-master`
`sh run_pipeline.sh test_data/polyA1Seq/PolyA1Seq_testdata.csv`
`conda activate sdmmej`
`cd sdmmej-master`
`sh run_pipeline.sh test_data/polyA1Seq/PolyA1Seq_testdata.csv`
It generates output files in a directory `PolyA1Seq_testdata_output` with the following output files
This generates output files in a directory `PolyA1Seq_testdata_output` with the following output files
- Outputs from Hifibr processing script
`PolyA1Seq_testdata_reclassified.csv` Same format input, but adds an “ID” column as well as a column for how the sequence was reclassified
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