diff --git a/README.md b/README.md index a399424..44148f1 100755 --- a/README.md +++ b/README.md @@ -50,7 +50,7 @@ conda install mamba -n base -c conda-forge Once installed ```mamba```, you are ready to build the CRISPRme environmet. To build the environment, type: ``` -mamba create -n crisprme python=3.8 crisprme -y +mamba create -n crisprme python=3.9.19 crisprme -y ``` To activate the environmment, type: @@ -72,7 +72,7 @@ mamba install crisprme== ``` For example: ``` -mamba install crisprme==2.1.2 +mamba install crisprme==2.1.5 ``` You can find the latest release indicated at the top of our [README](https://github.com/pinellolab/CRISPRme#crisprme). @@ -81,76 +81,8 @@ For OSX and Windows users is suggested to run CRISPRme via [Docker](https://www. If you plan to use CRISPRme via Docker on a Linux-based OS read and follow the instructions listed in the next section, skip it otherwise. -### Install Docker on Linux machines -Open a new terminal window and type: -``` -sudo apt-get update -``` - -To allow packages installation/update type over ```HTTPS``` channels: -``` -sudo apt-get install \ -apt-transport-https \ -ca-certificates \ -curl \ -gnupg-agent \ -software-properties-common -``` - -To add the docker key type: -``` -curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add - -``` - -To set the right Docker version for your system, type: -``` -sudo add-apt-repository \ -"deb [arch=amd64] https://download.docker.com/linux/ubuntu \ -$(lsb_release -cs) \ -Stable" -``` - -To make sure everythign is set to install Docker, refresh the repositories index again by typing: -``` -sudo apt-get update -``` - -To install Docker, type: -``` -sudo apt-get install docker-ce docker-ce-cli containerd.io -``` - -To test your Docker installation, type -``` -sudo docker run hello-world -``` - -If the following message is printed, Docker is correctly running on your machine: -![fig1](./docs/readme/hello-world-docker.png) - -To complete Docker's set up a few more steps are required. First, we need to create a Docker group. To do it, type: -``` -sudo groupadd docker -``` - -To add your current user to the Docker group, type: -``` -sudo usermod -aG docker $USER -``` - -Repeat the above command for all the user you plan to add to the Docker group (**NB** on most system you must be a ```sudo``` user to be able to do so). - -To make all changes effective, you will need to restart the machine or the environment. - -To test if the Docker group has been correctly configured, open a new terminal window and type: -``` -docker run hello-world -``` - -If the above "hello from Docker!" message is printed, Docker has been suceesfully installed and propoerly set on your machine. - -### Install CRISPRme docker image -Once obtained docker, open a new terminal window and type: +### Install CRISPRme using Docker +We assume you have already installed Docker on your system. Open a new terminal window and type: ``` docker pull pinellolab/crisprme ``` @@ -159,15 +91,13 @@ This command will download and install CRISPRme Docker image on your machine. ## Test CRISPRme To test your CRISPRme installation, open a new terminal window and type: ``` -wget https://www.dropbox.com/s/urciozkana5md0z/crisprme_test.tar.gz?dl=1 -O crisprme_test.tar.gz -tar -xvf crisprme_test.tar.gz +mkdir crisprme_test && cd crisprme_test +wget https://raw.githubusercontent.com/pinellolab/CRISPRme/refs/heads/main/crisprme_auto_test_conda.sh + ``` -This will download a folder containing some test data, to run and test CRISPRme. +This will download a script to download all the data necessary to run a full test using a single gRNA. Once downloaded, enter the folder by typing: -``` -cd crisprme_test -``` If you installed CRISPRme via ```conda```, test your conda installation by typing: ```