Add repo run script (2/N)

[rjcorb]

Purpose/implementation Section

What scientific question is your analysis addressing?

Closes #59. This PR adds a script run_analysis_modules.sh to generate results from all analysis modules in repo.

What was your approach?

What GitHub issue does your pull request address?

#59

Directions for reviewers. Tell potential reviewers what kind of feedback you are

soliciting.

Which areas should receive a particularly close look?

Please review bash script code and ensure it runs successfully. To run from root:

bash scripts/run_analysis_modules.sh

Is there anything that you want to discuss further?

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are

ready for review?

Results

What types of results are included (e.g., table, figure)?

What is your summary of the results?

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the
  project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to
  date.
• The analytical code is documented and contains comments.

[naqvia]

This failed to run complaining about ComplexHeatmap. I think you'll just need to load it.

root@0685d9fd2d0b:/home/rstudio/pbta-ancestry# bash scripts/run_analysis_modules.sh

/home/rstudio/pbta-ancestry/scripts
Run add-histologies

processing file: 01-add_histologies.Rmd

output file: 01-add_histologies.knit.md

/usr/local/bin/pandoc +RTS -K512m -RTS 01-add_histologies.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output 01-add_histologies.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpE7kdxx/rmarkdown-str54d62326199.html

Output created: 01-add_histologies.html
── Attaching core tidyverse packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.1 ✔ readr 2.1.4
✔ forcats 1.0.0 ✔ stringr 1.5.0
✔ ggplot2 3.4.2 ✔ tibble 3.2.1
✔ lubridate 1.9.2 ✔ tidyr 1.3.0
✔ purrr 1.0.1
── Conflicts ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::between() masks data.table::between()
✖ dplyr::filter() masks stats::filter()
✖ dplyr::first() masks data.table::first()
✖ lubridate::hour() masks data.table::hour()
✖ lubridate::isoweek() masks data.table::isoweek()
✖ dplyr::lag() masks stats::lag()
✖ dplyr::last() masks data.table::last()
✖ lubridate::mday() masks data.table::mday()
✖ lubridate::minute() masks data.table::minute()
✖ lubridate::month() masks data.table::month()
✖ lubridate::quarter() masks data.table::quarter()
✖ lubridate::second() masks data.table::second()
✖ purrr::transpose() masks data.table::transpose()
✖ lubridate::wday() masks data.table::wday()
✖ lubridate::week() masks data.table::week()
✖ lubridate::yday() masks data.table::yday()
✖ lubridate::year() masks data.table::year()
ℹ Use the conflicted package (http://conflicted.r-lib.org/) to force all conflicts to become errors
Error in library(ComplexHeatmap) :
there is no package called ‘ComplexHeatmap’
Execution halted

[jharenza]

Error in library(ComplexHeatmap) :
there is no package called ‘ComplexHeatmap’
Execution halted

also related to docker (I deleted my earlier comment because I didn't have the latest, but now I do and still not in there) - might want to manually push this - actually while we are at it, let's move the docker image to bixu...

[jharenza]

👍 this is good now!