commit

dabble-of-devops-bioanalyze · Aug 17, 2022 · bca876a · bca876a
1 parent 90896ea
commit bca876a
Showing 1 changed file with 37 additions and 11 deletions.
diff --git a/files/image-builder/scipy-bootstrap.yml b/files/image-builder/scipy-bootstrap.yml
@@ -61,18 +61,28 @@ phases:
               sudo yum-config-manager --enable epel
               sudo yum update -y; yum upgrade -y
               sudo yum group install -y 'Development Tools'
-              sudo yum install --quiet -y curl unzip wget git gitflow zsh \
-                Lmod \
-                sudo python3 pip3 amazon-efs-utils quota curl \
-                htop atop tree \
+
+              sudo yum install --quiet --skip-broken -y \
+                unzip wget git gitflow zsh
+
+              sudo yum install --quiet --skip-broken -y \
+                sudo python3-devel python3 pip3 amazon-efs-utils quota
+
+              sudo yum install --quiet --skip-broken -y htop atop tree
+
+              sudo yum install --quiet --skip-broken -y \
                 perl-devel perl-threads \
+
+              sudo yum install --quiet --skip-broken -y \
                 golang \
-                python3-devel s3fs-fuse \
+                s3fs-fuse \
                 openssl openssl-devel \
                 vsftpd \
                 libuuid-devel \
                 libseccomp-devel \
-                squashfs-tools \
+                squashfs-tools
+
+              sudo yum install --quiet --skip-broken -y \
                 singularity-runtime singularity
 
               curl -sL https://rpm.nodesource.com/setup_14.x | sudo bash -
@@ -81,6 +91,27 @@ phases:
               # nextflow needs java >= 11
               sudo amazon-linux-extras install -y java-openjdk11 R4
 
+              ################################################
+              # Install system packages - Fail safe
+              ################################################
+              sudo amazon-linux-extras install -y epel
+              sudo yum-config-manager --enable epel
+              sudo yum update -y; yum upgrade -y
+              sudo yum group install -y 'Development Tools'
+              sudo yum install --quiet --skip-broken -y curl unzip wget git gitflow zsh \
+                Lmod \
+                sudo python3 pip3 amazon-efs-utils quota curl \
+                htop atop tree \
+                perl-devel perl-threads \
+                golang \
+                python3-devel s3fs-fuse \
+                openssl openssl-devel \
+                vsftpd \
+                libuuid-devel \
+                libseccomp-devel \
+                squashfs-tools \
+                singularity-runtime singularity
+
               ################################################
               # Install Ansible
               ################################################
@@ -93,11 +124,6 @@ phases:
               ################################################
               sudo yum -y groups install "GNOME Desktop"
 
-              ################################################
-              # Install YQ
-              ################################################
-              yum -y groups install "GNOME Desktop"
-
               ################################################
               # Install YQ
               ################################################