Key resources supplementary table

[sjspielman]

This PR addresses this OpenPBTA-manuscript issue and Key Resources table for software. Per this comment, this table needs to be supplementary (not embedded in Methods) since there are > 10, so I'm filing in this repository where the supplementary tables are tracked.

An excel file was compiled with 4 sheets:

• All R packages in the Dockerfile. This list was derived using this approach. This includes all the 3.6.0 base R packages
• All Python libraries in the Dockerfile. This list was manually compiled.
• All command line software in the Dockerfile. This list was manually compiled.
• All software used in the workflows repository. This was compiled based on information in that repo's README, but some tool versions are not provided so they are marked "UNKNOWN" in the spreadsheet.

Questions for reviewers

• I have not included the linux dependencies in the docker file, like this stuff.

  curl \
  bzip2 \
  zlib1g \
  libbz2-dev \
  liblzma-dev \
  libreadline-dev

• Any comments on the spreadsheet organization?
• Does anyone know where to track down the versions of tools used in the workflows? Similarly are there tools used in the workflows that are not described in the README that need to be added?

[jharenza]

Does anyone know where to track down the versions of tools used in the workflows? Similarly are there tools used in the workflows that are not described in the README that need to be added?

@migbro can you please help with this? We are trying to wrap up the manuscript. Thank you!

[migbro]

Hmmm, sure can you give me a list of what is missing? I feel like most tools have a version, but in looking at those linux dependencies, that's really getting down in the weeds there. Those depend mostly on the defaults of the base image - like ubuntu18.04 vs 16.04, know what I mean?

[migbro]

I see a mention of " This was compiled based on information in that repo's README, but some tool versions are not provided so they are marked "UNKNOWN" in the spreadsheet," but I don't see that sheet.

[jharenza]

Oops, it is here: https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/1f5721bdc0a50aec89e4edc0600c6e1cb20c9cf1/tables/Key_Resources.xlxs

but @sjspielman can you change the extension to .xlsx

[jharenza]

Key_Resources.xlsx

@migbro - looks like MENDQC, VEP, bcftools

[sjspielman]

but @sjspielman can you change the extension to .xlsx

Oh boy that's quite the typo I made in there copying this file over!!

[migbro]

I've updated the sheet with software versions. Just a couple notes:

• In the cwl dir, https://github.com/d3b-center/OpenPBTA-workflows/blob/master/cwl/kfdrc_annot_vcf_sub_wf.cwl is a subworkflow wrapper, but has none of the tools. So if a person tried to download that and run as an app, it won't. If you want it all in one, we could export it from cavatica instead of what is in the repo. I can explain why that design if desired, but just a heads up.
• MendQC Dockerfile pulls from master, not a release. However, the file was created in December 2019, and also the image on dockerhub has that date, so seems to match v1.1.1 I put in the sheet based on the description here: https://github.com/UCSC-Treehouse/mend_qc/releases Key_Resources.xlsx

[sjspielman]

Thanks, @migbro !

[sjspielman]

I know the R package output is minimal code, but perhaps worth adding that to this script so we have the date run/output record.

Great idea! I'll write this to create sheet 1 and note remaining sheets are manual.

I'll change the file name for consistency, too.

[jaclyn-taroni]

I'll plan to look when the R code makes it into the table notebook. Please mention me when you're ready 😄

[sjspielman]

@jaclyn-taroni I updated this code so the table is entirely produced from the output_tables.Rmd notebook. A lot of this is manual data frames, but still much more reproducible than manually entered into an Excel.

[sjspielman]

@jaclyn-taroni Given the match between requirements.txt and Dockerfile, I ended up parsing the file directly. I think it makes sense to keep requirements.txt if only for others to use the file, if they want.