Add script to download methyl files

[zzgeng]

Purpose/implementation Section

What scientific question is your analysis addressing?

Add script to download v13 methylation-related files from AWS

What was your approach?

add download_methyl.sh in script folder.

What GitHub issue does your pull request address?

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

Which areas should receive a particularly close look?

script/download_methyl.sh

Is there anything that you want to discuss further?

No

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)?

bash script

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.

[jharenza]

Few notes:

1. If directory does not exist, this will fail. Can you add a chunk to check?
2. Can you make the script name download-methyl.sh with hyphen to conform to other script names?
3. Can you add a bit in the readme about this new script, what it is, how to download?

[jharenza]

@rjcorb I made some updates, can you test this on your end, esp since you do not have v13 on your computer currently?

[rjcorb]

@zzgeng @jharenza this runs fine when run within the scripts directory. But there are inconsistencies in which directories different scripts/ bash files need to be run from. For example, download-testing-files.sh needs to be run from root and not scripts/. I think following the code in scripts/generate-analysis-files.sh would allow this to be run from any directory:

# Set the working directory to the directory of this file
cd "$(dirname "${BASH_SOURCE[0]}")"

# If RUN_LOCAL is used, the time-intensive steps are skipped because they cannot
# be run on a local computer -- the idea is that setting RUN_LOCAL=1 will allow for
# local testing running/testing of all other steps
RUN_LOCAL=${RUN_LOCAL:-0}

# Get base directory of project
cd ..
BASEDIR="$(pwd)"
cd -

[rjcorb]

See above comment

[zzgeng]

@zzgeng @jharenza this runs fine when run within the scripts directory. But there are inconsistencies in which directories different scripts/ bash files need to be run from. For example, download-testing-files.sh needs to be run from root and not scripts/. I think following the code in scripts/generate-analysis-files.sh would allow this to be run from any directory:

# Set the working directory to the directory of this file
cd "$(dirname "${BASH_SOURCE[0]}")"

# If RUN_LOCAL is used, the time-intensive steps are skipped because they cannot
# be run on a local computer -- the idea is that setting RUN_LOCAL=1 will allow for
# local testing running/testing of all other steps
RUN_LOCAL=${RUN_LOCAL:-0}

# Get base directory of project
cd ..
BASEDIR="$(pwd)"
cd -

That's a very good suggestion! I've made changes accordingly. Thank you!

[jharenza]

Agree- Thanks @rjcorb