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update Wrangling Genomics to new dataset and software versions. #133

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merged 112 commits into from Feb 3, 2019

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commented Feb 3, 2019

This pull request updates the data set and software used in the Wrangling-Genomics lesson.

taylorreiter and others added some commits Jul 4, 2018

update cmds new versions of bcftools and samtools, reorder lessons, r…
…emove symlinking

Still need to update output of commands.
Need to update final exercise
update trimming commands and outputs, trim all files.
Note basename and gzip, and gunzip need to be added to Shell Genomics to support this lesson.
updated for new dataset!
samtools tview isn't working yet....not sure why, vcf looks good, and so does the ref genome.
Merge pull request #8 from data-lessons/tr-dev
Update gh-pages with new dataset, some story line, and some removed code that will go into shell genomics
add space after last file download
add space after download of file on line 58 to make everything download with the rest of the files
add info about long commands
Add info about when to have discussions to make use of time while long commands are running
start adding info about commands that don't run on
These are commands that don't run on purpose, adding info so instructors can be aware of them ahead of time rather than suspecting something is wrong when errors occur.

taylorreiter and others added some commits Feb 1, 2019

Merge pull request #33 from data-lessons/fpsom-patch-1
Updated README with PR#123 of the canonical
Merge pull request #34 from data-lessons/fpsom-patch-2
Updated index.md with PR#125 of canonical
Merge pull request #35 from data-lessons/fpsom-patch-3
Updated index.md with PR#125 of canonical
Merge pull request #36 from data-lessons/fpsom-patch-4
Updated index.md with PR#125 of canonical
Merge pull request #37 from data-lessons/fpsom-patch-5
Updated config.yml based on the PR#128 of the canonical
Merge pull request #38 from data-lessons/fpsom-patch-6
Updated README.md based on PR#129 from canonical
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