README change to adjust OS X install for md5sum

[cgreene]

Purpose/implementation Section

What scientific question is your analysis addressing?

None.

What was your approach?

Select a different distribution of md5sum that is compatible with the improvements added in #301

What GitHub issue does your pull request address?

#301

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

Which areas should receive a particularly close look?

Are the instructions clear enough for both new users and past participants who may have already installed via the other method?

Is there anything that you want to discuss further?

N/A

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

N/A

Results

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

N/A

What is your summary of the results?

N/A

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.

[cgreene]

This version of md5sum works with #301

[cgreene]

I had already downloaded the v11 files from previous testing, but it does find that the pbta-histologies.tsv file is unchanged:

Caseys-MacBook-Pro-2:OpenPBTA-analysis cgreene$ bash download-data.sh
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
Checking for unchanged files...
pbta-histologies.tsv
/Users/cgreene/OpenPBTA-analysis
Checking MD5 hashes...
pbta-histologies.tsv: OK
WGS.hg38.lancet.300bp_padded.bed: OK
WGS.hg38.lancet.unpadded.bed: OK
WGS.hg38.mutect2.unpadded.bed: OK
WGS.hg38.strelka2.unpadded.bed: OK
WGS.hg38.vardict.100bp_padded.bed: OK
WXS.hg38.100bp_padded.bed: OK
StrexomeLite_hg38_liftover_100bp_padded.bed: OK
StrexomeLite_Targets_CrossMap_hg38_filtered_chr_prefixed.bed: OK
pbta-snv-mutect2.vep.maf.gz: OK
pbta-snv-strelka2.vep.maf.gz: OK
pbta-snv-lancet.vep.maf.gz: OK
pbta-snv-vardict.vep.maf.gz: OK
pbta-cnv-cnvkit.seg.gz: OK
pbta-cnv-controlfreec.tsv.gz: OK
pbta-sv-manta.tsv.gz: OK
pbta-gene-expression-kallisto.polya.rds: OK
pbta-gene-expression-kallisto.stranded.rds: OK
pbta-gene-counts-rsem-expected_count.polya.rds: OK
pbta-gene-counts-rsem-expected_count.stranded.rds: OK
pbta-gene-expression-rsem-fpkm.polya.rds: OK
pbta-gene-expression-rsem-fpkm.stranded.rds: OK
pbta-isoform-counts-rsem-expected_count.polya.rds: OK
pbta-isoform-counts-rsem-expected_count.stranded.rds: OK
pbta-fusion-arriba.tsv.gz: OK
pbta-fusion-starfusion.tsv.gz: OK
independent-specimens.wgs.primary-plus.tsv: OK
independent-specimens.wgs.primary.tsv: OK
independent-specimens.wgswxs.primary-plus.tsv: OK
independent-specimens.wgswxs.primary.tsv: OK
pbta-gene-expression-rsem-tpm.polya.rds: OK
pbta-gene-expression-rsem-tpm.stranded.rds: OK
pbta-isoform-expression-rsem-tpm.polya.rds: OK
pbta-isoform-expression-rsem-tpm.stranded.rds: OK
pbta-fusion-putative-oncogenic.tsv: OK
pbta-gene-expression-rsem-fpkm-collapsed.polya.rds: OK
pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds: OK
pbta-snv-consensus-mutation-tmb.tsv: OK
pbta-snv-consensus-mutation.maf.tsv.gz: OK
Caseys-MacBook-Pro-2:OpenPBTA-analysis cgreene$

[jaclyn-taroni]

👍