Update homer macs

[rroutsong]

• Fix bug with DiffBind RMD and nRows
• Add new artifact protein_coding_genes.bed
• Implement new HOMER workflow
• deploy containerized homer environment (mounting /fdb in)

Release notes

• New Homer workflow on peak calling (different than differential binding outputs)
• Containerized homer environment

Release Options

• Major release (X.0.0)
• Minor release (0.X.0)
• Patch release (0.0.X)
• Skip release

[rroutsong]

Outputs can be examined at /data/OpenOmics/dev/datasets/outputs/test_new_homer_chromseek

[skchronicles]

Thank you for making this change for homer's bindpaths. I appreciate it! Just let us know when your testing is completed.

[tovahmarkowitz]

Ok, I made a few minor changes to the DiffBind Rmd scripts so they all match and hopefully now all use the correct if statements. Beyond that, I was hoping we could copy (not move) knownResults.txt so that we can look at it without untarring the big tarball. Is that possible/easy?

Otherwise, everything looks great to me. Thanks for all the hard work.

[skchronicles]

Thank you for updates to the block Rmarkdowns.

[skchronicles]

@tovahmarkowitz

Ok, I made a few minor changes to the DiffBind Rmd scripts so they all match and hopefully now all use the correct if statements. Beyond that, I was hoping we could copy (not move) knownResults.txt so that we can look at it without untarring the big tarball. Is that possible/easy?

Otherwise, everything looks great to me. Thanks for all the hard work.

I am okay with this. Do you know how large file maybe? Is it usually just a few MB max?

[skchronicles]

Okay, that knowResults.txt file should be relatively small. @rroutsong Can you please add a command to make a copy of that homer results file, and rename it to prevent collisions if the tarball is extracted. You can call it something like this for example: knowResults_macsNarrow.txt.

[tovahmarkowitz]

Just to be clear there are two htmls in each folder: homerResults.html and knownResults.html. I think there should only be knownResults.txt. The rest should have a variety of different other extensions like .tsv and .motifs. I am specifically only interested in the knownResults.txt file.

[rroutsong]

Just to be clear there are two htmls in each folder: homerResults.html and knownResults.html. I think there should only be knownResults.txt. The rest should have a variety of different other extensions like .tsv and .motifs. I am specifically only interested in the knownResults.txt file.

These are not very big and you are able to extract single files from a tar.gz:

[routsongrm@cn0052 macsNarrow] {14576996}$ du -sh 27_IFN0h_1_Sp100_S15_homer.tar.gz 
446K    27_IFN0h_1_Sp100_S15_homer.tar.gz

If you want to copy them somewhere please let me know where:

Homer output:

{root}/HOMER_chip/{sample}/macsNarrow/knownResults.txt[.html]

Is the current location

[skchronicles]

Thank you for that last update to create the tarball with an extra copies of the knowResults files.

[tovahmarkowitz]

Everything looks good to me!