berkeley-dsep-infra/datahub

Request python package X for class Y

ingolia opened this issue · 9 comments

ingolia commented

Package Name

MACS2

Hub URL

biology.datahub.berkeley.edu

Course Name

MCELLBI201B

Semester Details

Fall 2024

Installation Deadline

09/09

shaneknapp commented

this will be live on biology-staging.datahub.berkeley.edu in ~45m for testing. once it's deployed, please log in and confirm that the package is installed and working as intended.

thanks!

  • 🎉1
shaneknapp commented

ok it's live on biology-staging... looks like the package installed correctly, but you should definitely kick the tires a bit before we merge this to prod.

jovyan@jupyter-sknapp:~$ pip list | grep -i macs
MACS2                     2.2.9.1
ingolia commented
  • 👍1
ingolia commented
shaneknapp commented

please be sure you're logged in to https://biology-staging.datahub.berkeley.edu, and not https://biology.datahub.berkeley.edu

i checked, and you're logged in to 'prod', not 'staging'... :)

jovyan@jupyter-sknapp:~$ macs2 -h
usage: macs2 [-h] [--version] {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak} ...

macs2 -- Model-based Analysis for ChIP-Sequencing

positional arguments:
  {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak}
    callpeak            Main MACS2 Function: Call peaks from alignment results.
    bdgpeakcall         Call peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files
                        from MACS2 are accpetable.
    bdgbroadcall        Call broad peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph
                        files from MACS2 are accpetable.
    bdgcmp              Deduct noise by comparing two signal tracks in bedGraph. Note: All regions on the same chromosome in the bedGraph file should be continuous
                        so only bedGraph files from MACS2 are accpetable.
    bdgopt              Operations on score column of bedGraph file. Note: All regions on the same chromosome in the bedGraph file should be continuous so only
                        bedGraph files from MACS2 are accpetable.
    cmbreps             Combine BEDGraphs of scores from replicates. Note: All regions on the same chromosome in the bedGraph file should be continuous so only
                        bedGraph files from MACS2 are accpetable.
    bdgdiff             Differential peak detection based on paired four bedgraph files. Note: All regions on the same chromosome in the bedGraph file should be
                        continuous so only bedGraph files from MACS2 are accpetable.
    filterdup           Remove duplicate reads at the same position, then save the rest alignments to BED or BEDPE file. If you use '--keep-dup all option', this
                        script can be utilized to convert any acceptable format into BED or BEDPE format.
    predictd            Predict d or fragment size from alignment results. *Will NOT filter duplicates*
    pileup              Pileup aligned reads with a given extension size (fragment size or d in MACS language). Note there will be no step for duplicate reads
                        filtering or sequencing depth scaling, so you may need to do certain pre/post-processing.
    randsample          Randomly sample number/percentage of total reads.
    refinepeak          (Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of waston/crick tags. Inspired by SPP.

options:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

For command line options of each command, type: macs2 COMMAND -h
shaneknapp commented

how did the testing go? i'd like to merge to prod as we have a ton of commits that i'd like to clear out of the staging queue.

ingolia commented
  • 👍1
shaneknapp commented

awesome, i'll merge the changes to prod now. thanks!