Resources to add - Githubissues

fredhutchio / tfcb_2019

class materials for MCB517A through UW/Fred Hutch

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Resources to add #1

Closed k8hertweck closed 5 years ago

k8hertweck commented 5 years ago

[x] software installation instructions (copied and updated from last year)
[x] recommended reading list and other resources
[x] other information required by UW?
[x] Instructions for non-FH students (for obtaining HutchNetID)

rasi commented 5 years ago

@k8hertweck It will be useful to add install instructions for the tidyverse package (something like here). It is a long install and it will be necessary for running the example Rmarkdown document.

k8hertweck commented 5 years ago

Yes, I still need to finish the software install section. Here's the plan:

R: tidyverse and the following Bioconductor packages: GenomicRanges, VariantAnnotation, GenomeInfoDb, Rsamtools, ggbio, BSgenome.Hsapiens.UCSC.hg38
Windows Subsystem for Linux, perhaps also Git for Windows as a backup (if anyone is not running Windows 10)
Python: Biopython (not included in standard Anaconda installation)

rasi commented 5 years ago

Bioconductor and Biopython will be definitely useful. Perhaps everyone can chime in regarding the R and Python packages that they intend to use? Then we can make sure that they are installed by the first class.

gavinha commented 5 years ago

Hi @k8hertweck

For my content, we would need to use the following Bioconductor packages:

GenomicRanges
VariantAnnotation
GenomeInfoDb
Rsamtools
ggbio
BSgenome.Hsapiens.UCSC.hg38

I'll let you know if I can think of more.

Thanks, Gavin

k8hertweck commented 5 years ago

@rasi @gavinha I'm thinking it might be worth it to include the software install as install.packages() in the test script, to make sure folks get everything we need. What do you think of this?

rasi commented 5 years ago

@rasi @gavinha I'm thinking it might be worth it to include the software install as install.packages() in the test script, to make sure folks get everything we need. What do you think of this?

Yes, that is a good idea. The Bioconductor packages have a slightly different install command: https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html

k8hertweck commented 5 years ago

Yup, that's why I figured it would be easier to include in a script rather than trying to wrangle the class to get it done!