Commit 261be7da authored by Rebecca E Batorsky's avatar Rebecca E Batorsky
Browse files

test

parent b6e4236f
This diff is collapsed.
......@@ -8,10 +8,37 @@ Python 2.7
Python libraries: pandas
R >=3.5
R >=4.0
R libraries: tidyverse, Biostrings
**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"`
- Download repository (you will be prompted for password)
`git clone https://gitlab.tufts.edu/rbator01/sdmmej.git`
- 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
`source ~/.bash_profile`
- Create Conda environment
`conda config --add channels conda-forge`
`conda config --add channels r`
`conda config --add channels bioconda`
`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
`conda activate sdmmej`
`conda deactivate sdmmej`
**Pipeline Script**
This script takes the path to the HiFibr output file as the single command line argument.
......@@ -19,6 +46,8 @@ 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`
It generates output files in a directory `PolyA1Seq_testdata_output` with the following output files
......@@ -36,4 +65,4 @@ It generates output files in a directory `PolyA1Seq_testdata_output` with the fo
- Outputs from Insertoin script
`PolyA1Seq_testdatatestdata_insertion_consistency2.csv`
`PolyA1Seq_testdatatestdata_insertion_consistency_long2.csv`
`PolyA1Seq_testdatatestdata_insertion_alignment2.csv`
\ No newline at end of file
`PolyA1Seq_testdatatestdata_insertion_alignment2.csv`
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment