Path for monkeyPoo

[wmaguire-gladstone]

Verify path is setup correctly once in Wynton

MonkeyPipeline/bananas_agw.pm

Lines 810 to 814 in e010cd6

	dirExistsInConfigOrDie($cfg, 'monkeyPoo');
	if ($GLOBAL_DEV_MODE) { # MonkeyPoo directory should be changed to "/path/to/monkey/poo/dev_bin" instead of just "/path.../bin/"
	$cfg->{monkeyPoo} = dirname($cfg->{monkeyPoo}) . "/dev_" . basename($cfg->{monkeyPoo});
	dirExistsInConfigOrDie($cfg, 'monkeyPoo'); # check it AGAIN if we are in dev mode
	}

[AlexanderPico]

Here's another simply path swap that you'll know the answer to before we will :)

[wmaguire-gladstone]

Can you confirm for me that the monkeyPoo path is /data/applications/monkey/poo?

Contents:
0.danRer_sampleStudyDesign.txt mm10_ensemblGenes.bed
0.hg19_sampleStudyDesign.txt mm10_ensemblGeneWindows.bed
0.mm9_sampleStudyDesign.txt mm10_genomicBins.bed
0.NC_007605_sampleStudyDesign.txt mm10_genomicBinsID.bed
0.THESE_ARE_OLD_STUDY_DESIGN_FILES_DO_NOT_USE_WITH_MONKEY2.0 mm10_repeatMask.bed
bin_super_old/ mm10_symbolXref.txt
bin.tar.bz2 mm10_tssEnsemblGenes.bed
danRer7/ mm9_chrom.sizes
danRer7_chrom.sizes mm9_ENSTtoSymbol.txt
danRer7_ensembl_exons.bed mm9.fa
danRer7_ensembl_geneWindows.bed mm9.fa.fai
danRer7_ensembl_transcripts.bed mm9_genomicBins.bed
danRer7.fa mm9_genomicBinsID.bed
danRer7.fa.fai mm9_lncRNA_genes_noncodev4.bed
danRer7_genomicBins.bed mm9_lncRNA_transcripts_noncodev4.bed
danRer7_genomicBinsID.bed mm9_repeatMask.bed
danRer7_repeatMask.bed mm9_symbolXref.txt
danRer7_symbolXref.txt mm9_transcripts_ens67.bed
dm3_chrom.sizes mm9_tssEnsembl67.bed
dm3_geneWindows.bed mm9_tssEnsembl67_geneID.bed
dm3_genomicBins.bed mm9_ucsc_exons.bed
dm3_genomicBinsID.bed mm9_ucsc_geneWindows.bed
dm3_repeatMask.bed mm9_ucsc_transcripts.bed
dm3_symbolXref.txt NC_007605_chrom.sizes
dm6_chrom.sizes NC_007605_exons.bed
hg19_chrom.sizes NC_007605.fa
hg19.fa NC_007605.fa.fai
hg19.fa.fai NC_007605_geneWindows.bed
hg19_genomicBins.bed NC_007605_genomicBins.bed
hg19_genomicBinsID.bed NC_007605_genomicBinsID.bed
hg19_repeatMask.bed NC_007605_repeatMask.bed
hg19_symbolXref.txt NC_007605_symbolXref.txt
hg19_tssEnsembl_100bins20bpEach.bed NC_007605_transcripts.bed
hg19_tssEnsembl.bed NC_007605_tss.bed
hg19_tssEnsembl_named.bed Read_Distribution_BP.txt
hg19_ucsc_exons.bed Read_Distribution_ChIP-exo.txt
hg19_ucsc_geneWindows.bed Read_Distribution_default.txt
hg19_ucsc_transcripts.bed test_suite/
hg19_xref_ID2symbol.txt x.complete_adapters_to_trim.fasta
hg38_chrom.sizes x.defaultAdapters.txt

[wmaguire-gladstone]

/data/work/Code/alexgw/monkey_agw/bin

[wmaguire-gladstone]

path on wynton
/wynton/group/gladstone/biocore/monkey/bin

Need to update code

[wmaguire-gladstone]

Not sure there's actually any code to update here.

[dataMaster-Kris]

I cannot find the files at this Rigel location /data/applications/monkey/poo on Wynton. They are not in /wynton/group/gladstone/biocore/monkey/bin.

[wmaguire-gladstone]

Interesting, I can move those over. Based on the history of this issue, it looks like we determined /data/work/Code/alexgw/monkey_agw/bin was the directory that needed to be copied. Would you rather those be elsewhere and this take the place of /wynton/group/gladstone/biocore/monkey/bin? Or create a new dir /wynton/group/gladstone/biocore/monkey/poo and stage these under that?

[wmaguire-gladstone]

Should we add this to the repo?

[dataMaster-Kris]

The files in /data/applications/monkey/poo are meant for analyses other than RNA-seq. I haven't used them. @reubenthomas can you look into this? Thanks.