From f2c6d44dccfb5f693b66bc8fe23eb471a370afbb Mon Sep 17 00:00:00 2001
From: Marty Kandes <mkandes@sdsc.edu>
Date: Thu, 19 Aug 2021 03:45:18 +0000
Subject: [PATCH] Add support for CentOS/EPEL rpm-based yum install/remove of
Singularity
---
README.md | 2 +-
naked-singularity.sh | 136 +++++++++++++++++++++++++++++++------------
2 files changed, 99 insertions(+), 39 deletions(-)
diff --git a/README.md b/README.md
index 4337850..eacf637 100644
--- a/README.md
+++ b/README.md
@@ -60,7 +60,7 @@ University of California, San Diego
## Version
-1.8.5
+1.8.6
## Last Updated
diff --git a/naked-singularity.sh b/naked-singularity.sh
index 6d3ad5b..8c1ebb4 100755
--- a/naked-singularity.sh
+++ b/naked-singularity.sh
@@ -48,7 +48,8 @@ naked::install() {
local singularity_version='3.5.3'
local go_version='1.15.6'
- local -i use_rpm=1
+ local use_rpm='false'
+ local rpm_repo='epel'
local os_release_id=''
local os_release_version_id=''
@@ -64,9 +65,13 @@ naked::install() {
shift 2
;;
-r | --rpm )
- use_rpm=0
+ use_rpm='true'
shift 1
;;
+ -e | --enable-repo )
+ rpm_repo="${2}"
+ shift 2
+ ;;
*)
log::error "Command-line option ${1} not recognized or not supported."
return 1
@@ -166,40 +171,49 @@ naked::install() {
fi
- mkdir -p /tmp/go
- cd /tmp/go
+ if [[ "${os_release_id}" = 'centos' && "${use_rpm}" = 'true' ]]; then
+
+ log::output 'Installing Singularity ...'
+ yum -y install --enablerepo="${rpm_repo}" singularity-"${singularity_version}"
+
+ else # build and install singularity from source
- log::output 'Installing Go ...'
- export CGO_ENABLED=0
- wget https://dl.google.com/go/go1.4-bootstrap-20171003.tar.gz
- tar -xf go1.4-bootstrap-20171003.tar.gz
- mv go 1.4
- cd 1.4/src
- ./make.bash
+ mkdir -p /tmp/go
+ cd /tmp/go
- export GOROOT_BOOTSTRAP='/tmp/go/1.4'
+ log::output 'Installing Go ...'
+ export CGO_ENABLED=0
+ wget https://dl.google.com/go/go1.4-bootstrap-20171003.tar.gz
+ tar -xf go1.4-bootstrap-20171003.tar.gz
+ mv go 1.4
+ cd 1.4/src
+ ./make.bash
- cd /tmp/go
+ export GOROOT_BOOTSTRAP='/tmp/go/1.4'
- export CGO_ENABLED=1
- git clone https://go.googlesource.com/go "${go_version}"
- cd "${go_version}"
- git checkout "go${go_version}"
- cd src
- ./all.bash
+ cd /tmp/go
- export GOROOT="/tmp/go/${go_version}"
- export PATH="${GOROOT}/bin:${PATH}"
+ export CGO_ENABLED=1
+ git clone https://go.googlesource.com/go "${go_version}"
+ cd "${go_version}"
+ git checkout "go${go_version}"
+ cd src
+ ./all.bash
- cd /tmp
+ export GOROOT="/tmp/go/${go_version}"
+ export PATH="${GOROOT}/bin:${PATH}"
- log::output 'Installing Singularity ...'
- wget "https://github.com/hpcng/singularity/releases/download/v${singularity_version}/singularity-${singularity_version}.tar.gz"
- tar -xf "singularity-${singularity_version}.tar.gz"
- cd singularity
- ./mconfig #--prefix=/opt/singularity <- include prefix as used-defined option?
- make -C ./builddir
- make -C ./builddir install
+ cd /tmp
+
+ log::output 'Installing Singularity ...'
+ wget "https://github.com/hpcng/singularity/releases/download/v${singularity_version}/singularity-${singularity_version}.tar.gz"
+ tar -xf "singularity-${singularity_version}.tar.gz"
+ cd singularity
+ ./mconfig #--prefix=/opt/singularity <- include prefix as used-defined option?
+ make -C ./builddir
+ make -C ./builddir install
+
+ fi
# Prepend the path of the install directory of Singularity to PATH
# because not all secure_paths in /etc/sudoers may include it. If it
@@ -246,7 +260,7 @@ naked::install() {
naked::uninstall() {
local singularity_prefix='/usr/local'
- local -i use_rpm=1
+ local use_rpm='false'
local os_release_id=''
local os_release_version_id=''
@@ -258,7 +272,7 @@ naked::uninstall() {
shift 2
;;
-r | --rpm )
- use_rpm=0
+ use_rpm='true'
shift 1
;;
*)
@@ -276,18 +290,64 @@ naked::uninstall() {
return 1
fi
+ log::output 'Parsing /etc/os-release to identify operating system ...'
+ if [[ -f '/etc/os-release' ]]; then
+
+ grep '^ID=' /etc/os-release > /dev/null 2>&1
+ if [[ "${?}" -eq 0 ]]; then
+ grep '^ID=' /etc/os-release | grep '"' > /dev/null 2>&1
+ if [[ "${?}" -eq 0 ]]; then
+ os_release_id="$(grep '^ID=' /etc/os-release | cut -d '"' -f 2)"
+ else
+ os_release_id="$(grep '^ID=' /etc/os-release | cut -d '=' -f 2)"
+ fi
+ log::output "Operating system identified as ${os_release_id}."
+ else
+ log::error '/etc/os-release does not contain ID parameter.'
+ return 1
+ fi
+
+ grep '^VERSION_ID=' /etc/os-release > /dev/null 2>&1
+ if [[ "${?}" -eq 0 ]]; then
+ grep '^VERSION_ID=' /etc/os-release | grep '"' > /dev/null 2>&1
+ if [[ "${?}" -eq 0 ]]; then
+ os_release_version_id="$(grep '^VERSION_ID=' /etc/os-release | cut -d '"' -f 2)"
+ else
+ os_release_version_id="$(grep '^VERSION_ID=' /etc/os-release | cut -d '=' -f 2)"
+ fi
+ log::output "Operating system version identified as ${os_release_version_id}."
+ else
+ log::error '/etc/os-release does not contain VERSION_ID parameter.'
+ return 1
+ fi
+
+ else
+
+ log::error '/etc/os-release does not exist.'
+ return 1
+
+ fi
+
log::output 'Uninstalling Singularity ...'
- sudo rm -rf "${singularity_prefix}/libexec/singularity"
- sudo rm -rf "${singularity_prefix}/var/singularity"
- sudo rm -rf "${singularity_prefix}/etc/singularity"
- sudo rm -rf "${singularity_prefix}/bin/singularity"
- sudo rm -rf "${singularity_prefix}/bin/run-singularity"
- sudo rm -rf "${singularity_prefix}/etc/bash_completion.d/singularity"
+ if [[ "${os_release_id}" = 'centos' && "${use_rpm}" = 'true' ]]; then
+
+ yum -y remove singularity
+
+ else # remove source-based install
+
+ rm -rf "${singularity_prefix}/libexec/singularity"
+ rm -rf "${singularity_prefix}/var/singularity"
+ rm -rf "${singularity_prefix}/etc/singularity"
+ rm -rf "${singularity_prefix}/bin/singularity"
+ rm -rf "${singularity_prefix}/bin/run-singularity"
+ rm -rf "${singularity_prefix}/etc/bash_completion.d/singularity"
+
+ fi
log::output 'Checking if Singularity was uninstalled successfully ...'
which singularity
if [[ "${?}" -eq 0 ]]; then
- log:error 'Singularity was NOT uninstalled!'
+ log::error 'Singularity was NOT uninstalled!'
return 1
fi
--
GitLab