Hierarchy Selection

[jdimatteo]

Hierarchy Selection

[jdimatteo]

I updated the job on TOD, so that the hierarchical selections are in place. The table file is aIso loaded dynamically.

It should be self explanatory how to use it.

@bradnerComputation / Charles: could you please try this out and let me know what you think?

http://tod.dfci.harvard.edu/jenkins/job/Bam_Plot/build?delay=0sec

[jdimatteo]

@bradnerComputation / Charles: I just installed the updated hierarchy selection on TOD.

[jdimatteo]

Re-opening issue since a bug was found.

TOD jenkins/job/Bam_Plot/43 produced a graph with two plots, and the labels on the wrong plots. Build #43 log shows that the argument order is jumbled by bamPlotArgumentsFromTable.py:

python /ark/home/jenkins/scripts/bamPlotArgumentsFromTable.py /mnt/d0-0/share/bradnerlab/projects/masterBamTable.txt HG18,Multiple Myeloma,MM1S,MM1S_RNA_POL2_DMSO_2,,HG18,Multiple Myeloma,MM1S,MM1S_RNA_POL2_500nM_JQ1
+ arguments=/ifs/labs/bradner/bam/hg18/mm1s/05242012_D0WUYACXX_5.GGCTAC.hg18.bwt.sorted.bam,/ifs/labs/bradner/bam/hg18/mm1s/05242012_D0WUYACXX_4.CAGATC.hg18.bwt.sorted.bam -g HG18 -n MM1S_RNA_POL2_DMSO_2,MM1S_RNA_POL2_500nM_JQ1

The arguments should be set instead to the following:

arguments=/ifs/labs/bradner/bam/hg18/mm1s/05242012_D0WUYACXX_4.CAGATC.hg18.bwt.sorted.bam,/ifs/labs/bradner/bam/hg18/mm1s/05242012_D0WUYACXX_5.GGCTAC.hg18.bwt.sorted.bam -g HG18 -n MM1S_RNA_POL2_DMSO_2,MM1S_RNA_POL2_500nM_JQ1

[jdimatteo]

I just pushed out the bug fix to the repo, and confirmed that the order is now preserved. For example,

$ ./bamPlotArgumentsFromTable.py placeholder_data/masterBamTable.txt "HG18,Multiple Myee Myeloma,MM1S,MM1S_RNA_POL2_500nM_JQ1"
/ifs/labs/bradner/bam/hg18/mm1s/05242012_D0WUYACXX_4.CAGATC.hg18.bwt.sorted.bam,/ifs/labs/bradner/bam/hg18/mm1s/05242012_D0WUYACXX_5.GGCTAC.hg18.bwt.sorted.bam -g HG18 -n MM1S_RNA_POL2_DMSO_2,MM1S_RNA_POL2_500nM_JQ1
$

[jdimatteo]

I just updated the script on TOD, and the problem is now fixed. For example, TOD jenkins/job/Bam_Plot/80/console shows the same parameters as build 43, but now the order is correct.

[charlesylin]

Thanks!

The guys will test it tomorrow.

-Charles

Charles Y. Lin, Ph.D.
Dana-Farber Cancer Institute
Department of Medical Oncology
[email protected]:[email protected]
http://bradnerlab.com

On Wed, Oct 16, 2013 at 7:44 PM, jdimatteo [email protected] wrote:

I just updated the script on TOD, and the problem is now fixed now. For
example, TOD jenkins/job/Bam_Plot/80/console shows the same parameters as
build 43, but now the order is correct.

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