Singularity package investigation (again) reveals that self.stage.source_path...
package-investigation.mdThis is a debugging session for spack. The issue is that the self.stage.source_path changes (unexpectedly) in the middle of do_stage, and it's not clear why this happens. I'm at...
View ArticleAll the ways you can pull a Singularity container from shub.
singularity-pull-examples.mdWays to PullHow do you pull, my friend? Let me count the ways!1. Pull by Tag$ singularity pull shub://vsoch/singularity-images:latest 35.30 MiB / 35.30 MiB...
View ArticleAn example of how to put a really long error log (or similar) in markdown!...
markdown-details.mdLots of discussion, blardee boo, and here is my Dockerfile that is important to you!FROM debian:stretch-backports LABEL authors="@bnmnetp,@vsoch,@yarikoptic"# docker build -t...
View ArticleContainer Diff Examples
analyze_ubuntu.md$ container-diff analyze --type=apt ubuntu:16.04 -----Apt----- Packages found in ubuntu:16.04: NAME VERSION SIZE -adduser 3.113 nmu3ubuntu4 648K -apt 1.2.31 3.4M -base-files...
View ArticleSaving output to a file and printing to terminal
output_file.mdThis is executing a command to the container to list at the root (/) and then redirect stdout and stderr to "out.txt"$ singularity exec salad_latest.sif ls / 2>&1| tee out.txt bin...
View ArticleAn example of setting a custom environment variable already defined in the...
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View ArticleAn example of using the watchme psutils decorator to monitor resource usage...
result.json This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode...
View ArticleAn example multistage Dockerfile to install gvim and then throw the extra...
Dockerfile This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode...
View ArticleData.json served at...
data.json This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode...
View ArticleExample of using the monitor_gpu decorator
result.json This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode...
View ArticleApache with Singularity and without sudo
README.mdApache with SingularityStart with this recipeBootstrap: docker From:httpd:2.4.37 %startscript httpd-foreground Build the container:$ sudo singularity build apache.sif SingularityNext, make a...
View ArticleAn example Dockerfile using MicroSecurity scanner from AquaSec. You need to...
Dockerfile This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode...
View Articlenu 0.3.0 dependency output from running cargo-debstatus in the root of the...
cargo-debstatus-nu-0.3.0_10-17-2019.txt This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that...
View ArticleAn example of using rsync to backup three folders in Documents to an external...
backup.sh This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode...
View ArticleProvides a wrapper script to download a Snakemake Blob, and then extract to a...
download.py This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode...
View ArticleTesting run.sh script for Snakemake
run.sh This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode...
View ArticleA supporting script for a GitHub action to open a pull request
pull_request.sh This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode...
View ArticleApache Airflow Feedback 1/22/2020
AIRFLOW_FEEDBACK.mdAirflow FeedbackThis is feedback about contribution to Apache Airflow.BackgroundI first opened up a pull request in early March 2019 to add a Singularity operator to airflow. I am...
View ArticleDolmades Files
Dockerfile This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode...
View ArticleTesting Google Life Sciences updated download / upload script (will be put...
gls.py This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode...
View ArticleSnakemake Debugging on Google Cloud
snakemake-debugging.sh This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden...
View ArticleAn example for how to customize login-required (in this case, to use a...
decorators.py This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode...
View ArticleMy first logic program - am I a dinosaur (requires clingo)
dinosaur.lp This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode...
View ArticleClik here to view.
latex-jekyll-site.yaml
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View ArticleEmbedded fields in structs
main.go This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode...
View ArticleWhat do your pinned (or unpinned) requirements say about you?
README.mdWhat do your Python requirements say about you? 🤔I like living dangerouslyI am possibly bleeding right now.coreapiDjangoNovelty seekingNew bugs are good bugs. Old bugs are bad...
View ArticleTesting script for oras operator
entrypoint.sh This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode...
View Articlehotplug.sh
hotplug.sh This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode...
View Articlegenerate-artifact.sh
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