Elsayed-lab Singularity images

This is a ceph bucket hosted by UMIACS containing singularity images that are intended to be shared and contain analyses performed in various projects.

• cl_biopsies.sif: Analyses performed in the paper: "Consolidation of a molecular signature of healing in cutaneous leishmaniasis is achieved during the first ten days of treatment."
• cure_fail_host_analyses.sif: Analyses performed in the paper: "Innate biosignature of treatment failure in patients with cutaneous leishmaniasis."
• hpgltools.sif: Container of just the hpgltools package and runscript that can process arbitrary Rmd documents.
• tmrc2_analyses.sif: Analyses performed in the unnamed TMRC2 manuscript.
• macrophage_response.sif: The response of macrophages in the lab to two clinical strains. (Not yet uploaded)
• iprgc_translatome.sif: Searching for transcripts sent to and translated from the retina to axon projections in the suprachiasmatic nucleus and its sister location, the dorsal lateral geniculate nucleus. (Not yet uploaded)
• da_tracker.sif: Jacques' system for high-throughput cell segmentation and analysis.

I might need to ask for some more space, these images are kind of big.

Each of the above containers has its own repository and should be reasonably easily created by cloning it and invoking something along the lines of the following:

git clone https://github.com/abelew/hpgltools_singularity.git
cd hpgltools_singularity
make

With that in mind, here are the repositories for the above images:

• Cutaneous Leishmaniasis biopsies
• hpgltools
• Macrophage responses to two strains
• Cure vs. fail host resposes

The following shell block contains the commands to create an html version of this document from the org source and upload it (and the .sif containers) to the umiacs ceph instance.

pandoc --from=org --to=html --output index.html index.org

rclone --progress sync ./ elsayedlab:elsayedsingularity/

Note to self, evaluating the above block when using org-html-export is super-weird because it ends up generating itself from within itself and in theory could cause a loop. When I tried this hoping to be entertained by shenanigans, it behaved with perfect sanity. So I guess this is good and that the org-babel authors are smarter than I would be in their position. (Now that I think about it, I would need to add an elisp source block containing (org-html-export-to-html) for shenanigans)

Conversely, one can just invoke M-x org-html-export-to-html from within this document.