From 87a321a6b83ec9bdf6fc08e500d99b19abdae513 Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Wed, 19 Apr 2023 16:32:59 +0200
Subject: [PATCH 1/2] modifications

---
 packer_templates/pkr-builder.pkr.hcl          |  1 +
 packer_templates/pkr-variables.pkr.hcl        |  4 +-
 .../scripts/ubuntu/biocore_ubuntu.sh          | 45 +++++++++++++++++++
 3 files changed, 48 insertions(+), 2 deletions(-)
 create mode 100644 packer_templates/scripts/ubuntu/biocore_ubuntu.sh

diff --git a/packer_templates/pkr-builder.pkr.hcl b/packer_templates/pkr-builder.pkr.hcl
index c586f3ada..bd7d38735 100644
--- a/packer_templates/pkr-builder.pkr.hcl
+++ b/packer_templates/pkr-builder.pkr.hcl
@@ -106,6 +106,7 @@ locals {
             "${path.root}/scripts/_common/parallels.sh",
             "${path.root}/scripts/${var.os_name}/hyperv_${var.os_name}.sh",
             "${path.root}/scripts/${var.os_name}/cleanup_${var.os_name}.sh",
+            "${path.root}/scripts/${var.os_name}/biocore_${var.os_name}.sh",
             "${path.root}/scripts/_common/minimize.sh"
             ] : (
             var.os_name == "fedora" ? [
diff --git a/packer_templates/pkr-variables.pkr.hcl b/packer_templates/pkr-variables.pkr.hcl
index 666c2fc30..72416d754 100644
--- a/packer_templates/pkr-variables.pkr.hcl
+++ b/packer_templates/pkr-variables.pkr.hcl
@@ -158,8 +158,8 @@ variable "vboxmanage" {
       "{{.Name}}",
       "--audio",
       "none",
-      "--nat-localhostreachable1",
-      "on",
+      #"--nat-localhostreachable1",
+      #"on",
     ]
   ]
 }
diff --git a/packer_templates/scripts/ubuntu/biocore_ubuntu.sh b/packer_templates/scripts/ubuntu/biocore_ubuntu.sh
new file mode 100644
index 000000000..b5b9cbcc0
--- /dev/null
+++ b/packer_templates/scripts/ubuntu/biocore_ubuntu.sh
@@ -0,0 +1,45 @@
+#!/bin/sh -eux
+export DEBIAN_FRONTEND=noninteractive
+
+echo "update the package list"
+apt-get -y update;
+
+echo "install desktop packages"
+apt-get -y install lightdm ubuntu-desktop;
+
+echo "install deps for bioinformatics tools"
+apt-get -y install java perl python git wget curl;
+
+echo "install Docker CE"
+# https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/#install-docker
+apt-get -y remove docker docker-engine docker.io containerd runc;
+apt-get -y install apt-transport-https ca-certificates curl software-properties-common;
+
+install -m 0755 -d /etc/apt/keyrings
+curl -fsSL https://download.docker.com/linux/ubuntu/gpg | gpg --dearmor -o /etc/apt/keyrings/docker.gpg
+chmod a+r /etc/apt/keyrings/docker.gpg
+
+echo \
+  "deb [arch="$(dpkg --print-architecture)" signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu \
+  "$(. /etc/os-release && echo "$VERSION_CODENAME")" stable" | \
+  tee /etc/apt/sources.list.d/docker.list > /dev/null
+
+apt-get -y update
+apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
+
+usermod -aG docker $USER
+usermod -aG docker vagrant
+
+echo "install Apptainer"
+apt-get -y install \
+    squashfs-tools \
+    squashfuse \
+    fuse2fs \
+    fuse-overlayfs \
+    fakeroot \
+    cryptsetup
+
+TEMP_DEB="$(mktemp)" &&
+wget -O "$TEMP_DEB" 'https://github.com/apptainer/apptainer/releases/download/v1.1.7/apptainer_1.1.7_amd64.deb' &&
+dpkg -i "$TEMP_DEB"
+rm -f "$TEMP_DEB"

From a7089034b26d11937d2403993f3fa5a790344681 Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toniher@cau.cat>
Date: Wed, 19 Apr 2023 23:46:44 +0200
Subject: [PATCH 2/2] adding packages!

---
 packer_templates/scripts/ubuntu/biocore_ubuntu.sh | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/packer_templates/scripts/ubuntu/biocore_ubuntu.sh b/packer_templates/scripts/ubuntu/biocore_ubuntu.sh
index b5b9cbcc0..929d72dbb 100644
--- a/packer_templates/scripts/ubuntu/biocore_ubuntu.sh
+++ b/packer_templates/scripts/ubuntu/biocore_ubuntu.sh
@@ -5,14 +5,14 @@ echo "update the package list"
 apt-get -y update;
 
 echo "install desktop packages"
-apt-get -y install lightdm ubuntu-desktop;
+apt-get -y install lightdm ubuntu-desktop firefox;
 
 echo "install deps for bioinformatics tools"
-apt-get -y install java perl python git wget curl;
+apt-get -y install default-jre default-jdk perl python3 git wget curl;
 
 echo "install Docker CE"
 # https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/#install-docker
-apt-get -y remove docker docker-engine docker.io containerd runc;
+# apt-get -y remove docker docker-engine docker.io containerd runc;
 apt-get -y install apt-transport-https ca-certificates curl software-properties-common;
 
 install -m 0755 -d /etc/apt/keyrings
@@ -25,7 +25,7 @@ echo \
   tee /etc/apt/sources.list.d/docker.list > /dev/null
 
 apt-get -y update
-apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
+apt-get -y install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
 
 usermod -aG docker $USER
 usermod -aG docker vagrant
@@ -37,7 +37,8 @@ apt-get -y install \
     fuse2fs \
     fuse-overlayfs \
     fakeroot \
-    cryptsetup
+    cryptsetup \
+    uidmap
 
 TEMP_DEB="$(mktemp)" &&
 wget -O "$TEMP_DEB" 'https://github.com/apptainer/apptainer/releases/download/v1.1.7/apptainer_1.1.7_amd64.deb' &&