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shenlab-sinai / ngsplot

Quick mining and visualization of NGS data by integrating genomic databases
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NGS Plot error #32

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
I am using NGS Plot on a local galaxy instance. It gives me a error 
error
An error occurred with this dataset:
zip error: Nothing to do! (data.zip) mv: cannot stat `data.zip': No such file
or directory

Can you please help.

warm regards,
Amit.

Original issue reported on code.google.com by amitpand...@gmail.com on 9 Sep 2014 at 11:00

GoogleCodeExporter commented 9 years ago 
Name:   ngs.plot on data 1
Created:    Tue Sep 9 11:04:43 2014 (UTC)
Filesize:   0 bytes
Dbkey:  hg19
Format: pdf
Galaxy Tool Version:    1.0.0
Tool Version:   
Tool Standard Output:   stdout
Tool Standard Error:    stderr
Tool Exit Code: 1
API ID: 6f91353f3eb0fa4a
Full Path:  /bioappl/bin/galaxy-dist/database/files/000/dataset_97.dat
Job Command-Line:   bash 
/bioappl/bin/galaxy-dist/tools/ngsplot/ngs.plot.tss_tes.sh hg19 tss 
/bioappl/bin/galaxy-dist/database/files/000/dataset_88.dat 
/bioappl/bin/galaxy-dist/database/files/000/dataset_99.dat 
/bioappl/bin/galaxy-dist/database/files/000/dataset_97.dat 
/bioappl/bin/galaxy-dist/database/files/000/dataset_98.dat "Noname" refseq 2000 
1 total 100 150 20 1 0 0.02 1 0

Original comment by amitpand...@gmail.com on 9 Sep 2014 at 11:07

pajanne commented 8 years ago

Same issue here, and unable to find a solution easily. Same error in Galaxy and at the command line. perl /data/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ngsplot/ngsplot/f7debdafc7cb/ngsplot/ngsplot_galaxytoolshed_v.10/ngsplot_main/runNGSplot.pl hg19 tss na na flanking_region_size 2000 1 no /data/galaxy/files/035/dataset_35026.dat na no -1 plot1 150 green refseq 1 total NA NA NA 100 20 1 0 0.02 1 0 /data/galaxy/files/035/dataset_35068.dat /data/galaxy/files/035/dataset_35066.dat /data/galaxy/files/035/dataset_35067.dat

cp: cannot stat `data.zip': No such file or directory

pajanne commented 8 years ago

Ran more tests. Get this to work fine: ngs.plot.r -G hg19 -R tss -C example.bam/hesc.H3k4me3.1M.bam -O k4.test

Then uploaded hesc.H3k4me3.1M.bam into galaxy but still get the same error as well as running it on the command line: cp: cannot stat `data.zip': No such file or directory

Could the problem be in the runNGSplot.pl wrapper? Many thanks.

pajanne commented 8 years ago

I've commented out the line system($cmd2); in runNGSplot.pl which makes it works in Galaxy but all outputs are empty.

Running it at the command line will fill these PDF outputs but not the zip...

It would be great to get a fix to make it works in galaxy, and I am more than happy to test it whenever is available. Many thanks.

mictadlo commented 8 years ago

hi, we are getting cp cannot stat 'data.zip': no such file or directory. Any update on this issue?

Thank you in advance.

Mic