Merge pull request #13 An error occurred from fp9695253/master

Add virtual environment installation step, make users passwordless sudoer

tasks_sudo/get_docker.sh

@@ -1,5 +1,14 @@
 #!/bin/bash
 
+if [ "$(id -u)" != "0" ]; then
+    echo ""
+    echo ""
+    echo "This script should be run as root."
+    echo ""
+    echo ""
+    exit 1;
+fi
+
 bash <( curl https://get.docker.com/ )
 
 usermod -aG docker ubuntu

tasks_sudo/get_docker_compose.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+if [ "$(id -u)" != "0" ]; then
+    echo ""
+    echo ""
+    echo "This script should be run as root."
+    echo ""
+    echo ""
+    exit 1;
+fi
+
+curl -L "https://github.com/docker/compose/releases/download/1.22.0/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
+chmod +x /usr/local/bin/docker-compose
+

tasks_sudo/make_user.sh

@@ -14,7 +14,7 @@ fi
 
 set -x
 
-USERNAME="matomo"
+USERNAME="florence"
 
 sudo mkdir -p /home/${USERNAME}
 
@@ -22,6 +22,8 @@ sudo useradd -s /bin/bash -d /home/$USERNAME $USERNAME
 sudo usermod -a -G ubuntu $USERNAME
 sudo usermod -a -G sudo $USERNAME
 
+echo "${REGUSER} ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/${REGUSER}
+
 # copy the user init script
 sudo wget https://raw.githubusercontent.com/dahak-metagenomics/dahak-yeti/master/tasks_user/user_init.sh -O /home/$USERNAME/user_init.sh
 sudo chown -R ${USERNAME}:${USERNAME} /home/${USERNAME}

tasks_sudo/sudo_init.sh

@@ -1,5 +1,14 @@
 #!/bin/bash
 
+if [ "$(id -u)" != "0" ]; then
+    echo ""
+    echo ""
+    echo "This script should be run as root."
+    echo ""
+    echo ""
+    exit 1;
+fi
+
 if [[ "$#" -eq 1 ]]
 then
 
@@ -14,6 +23,7 @@ then
     ./gen_ssh_keys.sh
     ./set_machine_name.sh $1
     ./get_docker.sh
+    ./get_docker_compose.sh
     ./make_temp.sh
     ./install_singularity.sh &> /tmp/install_singularity_log
 

tasks_user/install_virtualenv.py

@@ -0,0 +1,39 @@
+#!/usr/bin/env python3
+import os, sys
+import getpass
+import tempfile
+import subprocess
+
+"""
+Install Virtualenv
+"""
+
+def install_venv():
+    user = getpass.getuser()
+
+    if(user=="root"):
+        raise Exception("You are root - you should run this script as a normal user.")
+    else:
+
+        print("Installing snakemake...")
+
+        pyenvbin = os.environ['HOME']
+        condabin = pyenvbin+"/.pyenv/shims/conda"
+        pipbin = pyenvbin+"/.pyenv/shims/pip"
+
+        print(" - Installing virtualenv")
+        rc = subprocess.call([pipbin,"install","virtualenv"])
+        if(rc != 0):
+            raise Exception()
+
+
+        print("     ~~*~~ ~~*~~ ~~*~~ SUCCESS! ~~*~~ ~~*~~ ~~*~~\n")
+        print("     Snakemake is now installed.")
+        print("     Test that snakemake is working using the following one-liner:\n")
+        print("         virtualenv vp && rm -fr vp")
+        print()
+
+
+if __name__=="__main__":
+    install_venv()
+

tasks_user/user_init.sh

@@ -19,4 +19,5 @@ cd ../
 ./install_pyenv.py
 . ~/.bash_profile
 ./activate_conda.py
+./install_virtualenv.py
 ./install_snakemake.py