Easy-Prime Installation steps¶
Summary¶
Installation of Easy-Prime is really easy via conda, however, you might experience errors due to lower conda version problem. Please make sure that you have conda installed and conda version >= 4.9.
Note
Easy-Prime is only available on Linux or Mac. For installation via conda, make sure conda version >= 4.9.
Steps¶
The installation may take 20 min.
Stage 1. Type the installation command¶
conda create -n easy_prime -c cheng_lab easy_prime
Please note that -n ENV_NAME, the ENV_NAME can be anything strings without space. -c cheng_lab easy_prime means installation the compiled conda package (namely easy_prime) from cheng_lab channel.
Stage 2. Type y to start installation¶
Once you have typed in the conda create command, the conda program will start to gather information, for example, informing you about new conda version. Then it tells you a “Package Plan”, for new packages to be downloaded and installed.
Now, type y and enter.
Stage 3. Waiting for installation, may take 20 min¶
Stage 4. Installation is completed¶
The terminal says, “To activate, use conda activate easy_prime”.
To use conda activate or source activate depends on the operating system. In Mac and Linux, please use source activate easy_prime.
Stage 5. Print Easy_prime help message¶
Type, easy_prime -h
FAQ¶
Can Easy-Prime be installed in Windows?¶
No. It is currently impossible because the ViennaRNA package is not available in Windows. We might develop a Docker version for Easy-Prime in the future so that users in any OS can use Easy-Prime.
Can Easy-Prime be installed via lower conda version?¶
Yes. It is possible but can be time-consuming. You can install the following dependencies via conda (some may still need higher conda version)and then install Easy-Prime via pip install easy-prime.
- python
- bedtools
- matplotlib
- pandas
- xgboost
- scikit-learn
- viennarna
- joblib
- pyyaml
- scikit-bio
- biopython
- mechanize
- dna_features_viewer
- dash
- dash-bio
- dash-core-components
- jupyter_dashboards
- plotly