From f7da13c5d198e001bd78233f3a8e18b6e826dffe Mon Sep 17 00:00:00 2001 From: Ivan Cao-Berg Date: Thu, 18 Apr 2024 18:14:11 -0400 Subject: [PATCH] Added version 6.0 --- 6.0/Dockerfile | 10 +++ 6.0/Singularity | 16 ++++ 6.0/build.sh | 19 +++++ 6.0/dbuild.sh | 6 ++ 6.0/gnuplot | 18 ++++ 6.0/modulefile.lua | 40 +++++++++ 6.0/rbuild.sh | 19 +++++ 6.0/test.sh | 4 + CONTRIBUTING.md | 52 ++++++++++++ LICENSE | 202 +++++++++++++++++++++++++++++++++++++++++++++ README.md | 51 ++++++++++++ 11 files changed, 437 insertions(+) create mode 100644 6.0/Dockerfile create mode 100644 6.0/Singularity create mode 100755 6.0/build.sh create mode 100755 6.0/dbuild.sh create mode 100755 6.0/gnuplot create mode 100644 6.0/modulefile.lua create mode 100755 6.0/rbuild.sh create mode 100755 6.0/test.sh create mode 100644 CONTRIBUTING.md create mode 100644 LICENSE create mode 100644 README.md diff --git a/6.0/Dockerfile b/6.0/Dockerfile new file mode 100644 index 0000000..d3739bd --- /dev/null +++ b/6.0/Dockerfile @@ -0,0 +1,10 @@ +FROM alpine:edge + +LABEL "MAINTAINER"="icaoberg" +LABEL "EMAIL"="icaoberg@psc.edu" +LABEL "SUPPORT"="help@psc.edu" +LABEL "REPOSITORY"="http://github.com/brain-image-library/singularity-gnuplot" +LABEL "COPYRIGHT"="Copyright © 2024 Pittsburgh Supercomputing Center. All Rights Reserved." +LABEL "VERSION"="6.0" + +RUN apk add --update gnuplot diff --git a/6.0/Singularity b/6.0/Singularity new file mode 100644 index 0000000..e78e693 --- /dev/null +++ b/6.0/Singularity @@ -0,0 +1,16 @@ +Bootstrap: docker +From: alpine:edge + +%labels + AUTHOR icaoberg + EMAIL icaoberg@psc.edu + SUPPORT help@psc.edu + WEBSITE http://github.com/brain-image-library/singularity-gnuplot + COPYRIGHT Copyright © 2024 Pittsburgh Supercomputing Center. All Rights Reserved. + VERSION 6.0-patch-level-0 + +%post + apk add --update gnuplot + +%runscript + gnuplot "$@" diff --git a/6.0/build.sh b/6.0/build.sh new file mode 100755 index 0000000..e9f8792 --- /dev/null +++ b/6.0/build.sh @@ -0,0 +1,19 @@ +#!/bin/bash + +# Copyright © 2024 Pittsburgh Supercomputing Center. +# All Rights Reserved. + +IMAGE=singularity-gnuplot-6.0.sif +DEFINITION=Singularity + +if [ -f $IMAGE ]; then + rm -fv $IMAGE +fi + +sudo singularity build $IMAGE $DEFINITION + +if [ -f $IMAGE ]; then + exit 0 +else + exit 1 +fi diff --git a/6.0/dbuild.sh b/6.0/dbuild.sh new file mode 100755 index 0000000..7177ef3 --- /dev/null +++ b/6.0/dbuild.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +# Copyright © 2024 Pittsburgh Supercomputing Center. +# All Rights Reserved. + +docker build -t icaoberg/gnuplot:6.0 . diff --git a/6.0/gnuplot b/6.0/gnuplot new file mode 100755 index 0000000..92fd06f --- /dev/null +++ b/6.0/gnuplot @@ -0,0 +1,18 @@ +#!/bin/bash + +VERSION=6.0 +PACKAGE=gnuplot +TOOL=gnuplot +DIRECTORY=$(dirname $0) + +STORAGES=(/bil /scratch /local) + +OPTIONS="" +for STORAGE in "${STORAGES[@]}" +do + if [ -d "$STORAGE" ]; then + OPTIONS=$OPTIONS" -B $STORAGE" + fi +done + +singularity exec $OPTIONS $DIRECTORY/singularity-$PACKAGE-$VERSION.sif $TOOL "$@" diff --git a/6.0/modulefile.lua b/6.0/modulefile.lua new file mode 100644 index 0000000..865688e --- /dev/null +++ b/6.0/modulefile.lua @@ -0,0 +1,40 @@ +-- +-- gnuplot 6.0 modulefile +-- +-- "URL: https://www.psc.edu/resources/software" +-- "Category: Other" +-- "Description: gnuplot is a command-line and GUI program that can generate two- and three-dimensional plots of functions, data, and data fits." +-- "Keywords: singularity utilities" + +whatis("Name: gnuplot") +whatis("Version: 6.0") +whatis("Category: Other") +whatis("URL: https://www.psc.edu/resources/software") +whatis("Description: gnuplot is a command-line and GUI program that can generate two- and three-dimensional plots of functions, data, and data fits.") + +help([[ +gnuplot is a command-line and GUI program that can generate two- and three-dimensional plots of functions, data, and data fits. + +To load the module type + +> module load gnuplot/6.0 + +To unload the module type + +> module unload gnuplot/6.0 + +Documentation +------------- +For help, type + +> gnuplot --help + +Tools included in this module are + +* gnuplot +]]) + +local package = "gnuplot" +local version = "6.0" +local base = pathJoin("/bil/packages",package,version) +prepend_path("PATH", base) diff --git a/6.0/rbuild.sh b/6.0/rbuild.sh new file mode 100755 index 0000000..bbee966 --- /dev/null +++ b/6.0/rbuild.sh @@ -0,0 +1,19 @@ +#!/bin/bash + +# Copyright © 2024 Pittsburgh Supercomputing Center. +# All Rights Reserved. + +IMAGE=singularity-gnuplot-6.0.sif +DEFINITION=Singularity + +if [ -f $IMAGE ]; then + rm -fv $IMAGE +fi + +singularity build --remote $IMAGE $DEFINITION + +if [ -f $IMAGE ]; then + exit 0 +else + exit 1 +fi diff --git a/6.0/test.sh b/6.0/test.sh new file mode 100755 index 0000000..88a723f --- /dev/null +++ b/6.0/test.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +set -x +tree . diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..798ef39 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,52 @@ +# Contributing to this repository +If you are a [PSC](https://www.psc.edu/staff-directory/) staff or intern, when contributing to this repository, please first request permission for changes you wish to make via issue, email, milestone, Slack or any other method you see fit. + +If you are a collaborator or a community member, when contributing to this repository, please fork this repository and create a [pull request](https://docs.github.com/en/github/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests) when appropiate. + +# Checklist +Please make sure the listed files are listed within the repository and update them as needed + +1. `README.md` +2. `LICENSE` +3. Github Action folder `.github` + +For each version, you will create a separate folder. For each version, create or update + +1. `Singularity` definition file, one per version +2. Build scripts `build.sh` and `rbuild.sh`, one pair per version +3. LMOD `modulefile.lua` file, one file per version +4. Test script `test.sh`, one file per version + +# Ready to make changes? Open your own branch +Use a branch to isolate development work without affecting other branches in the repository. Each repository has one default branch, and can have multiple other branches. You can merge a branch into another branch using a pull request. +To learn how to create a branch click [here](https://docs.github.com/en/desktop/contributing-and-collaborating-using-github-desktop/making-changes-in-a-branch/managing-branches ). + +# Use a Consistent Coding Style +For this project we will follow the [Google Style Guides](https://google.github.io/styleguide/) for Shell and Python (and others if necessary). + +* 2 spaces for indentation rather than tabs +* You can try running npm run lint for style unification + +# Report bugs using Github's issues +We use GitHub issues to track public bugs. Report a bug by opening a new issue. + +For instructions, please click [here](https://docs.github.com/en/issues/tracking-your-work-with-issues/creating-issues/creating-an-issue). + +# Pull request process +1. Ensure any install Git application and a text editor on your computing device. +2. Have the right access to the desired repository. +3. Update the README.md using the text editor with details of changes to the interface, this includes new environment variables, exposed ports, useful file locations and container parameters. +4. Increase the version numbers in any examples files and the README.md to the new version that this Pull Request would represent. +5. Commit changes to main after you fetch origin then push origin through Git. Refresh the repository on Github webpage. +6. You may merge the Pull Request in once you have the sign-off of two other developers, or if you do not have permission to do that, you may request the second reviewer to merge it for you. + +# Windows +his site can be developed on Windows, however a few potential gotchas need to be kept in mind +1. Regular expressions. Windows uses `\r\n` for line endings, while Unix based systems use `\n`. Therefore when working on Regular Expressions, use `\r?\n` instead of `\n` in order to support both environments. The Node.js os.EOL property can be used to get an OS-specific end-of-line marker. +2. Paths. Windows systems use `\` for the path separator, which would be returned by `path.join` and others. You could use `path.posix`, `path.posix.join`, etc. and the slash module, if you need forward slashes - like for constructing URLs - or ensure your code works with either. +3. Bash. Not every Windows developer has a terminal that fully supports Bash, so it's generally preferred to write scripts in JavaScript instead of Bash. + +# Support +Please email [help@psc.edu](help@psc.edu) for support requests. + +[![Logo](https://developer.nvidia.com/sites/default/files/logos/psc_logo.png)](https://github.com/orgs/pscedu) diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..d645695 --- /dev/null +++ b/LICENSE @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/README.md b/README.md new file mode 100644 index 0000000..104e84f --- /dev/null +++ b/README.md @@ -0,0 +1,51 @@ +![Status](https://github.com/brain-image-library/singularity-gnuplot/actions/workflows/main.yml/badge.svg) +![Status](https://github.com/brain-image-library/singularity-gnuplot/actions/workflows/pretty.yml/badge.svg) +![Issue](https://img.shields.io/github/issues/brain-image-library/singularity-gnuplot) +![forks](https://img.shields.io/github/forks/brain-image-library/singularity-gnuplot) +![Stars](https://img.shields.io/github/stars/brain-image-library/singularity-gnuplot) +![License](https://img.shields.io/github/license/brain-image-library/singularity-gnuplot) + +# singularity-gnuplot +![Plot](http://gnuplot.sourceforge.net/demo/animate2.1.gif) + +Singularity recipe for [gnuplot](http://gnuplot.info/). + +## Installing the container on BRAIN +Copy the + +* `SIF` file +* and the `gnuplot` script + +to `/bil/packages/gnuplot/5.4`. + +Copy the file `modulefile.lua` to `/bil/modulefiles/gnuplot` as `5.4.lua`. + +## Building the image using the recipe +### To build the image locally +Run the script `build.sh` to build image locally. + +``` +bash ./build.sh +``` + +### To build the image remotely +Run the script `rbuild.sh` to build image remotely. + +``` +bash ./rbuild.sh +``` + +## To run tests +To run the available tests, run the command + +``` +bash ./test.sh +``` + +### Comment +This container was built to be used with the Remote Desktop Application using the OpenOnDemand instance for the Brain Image Library. + +--- +Copyright © 2024 Pittsburgh Supercomputing Center. All Rights Reserved. + +The [Biomedical Applications Group](https://www.psc.edu/biomedical-applications/) at the [Pittsburgh Supercomputing Center](http://www.psc.edu) in the [Mellon College of Science](https://www.cmu.edu/mcs/) at [Carnegie Mellon University](http://www.cmu.edu).