Looking for hg19.AS.STRUCTURE.COMPILED.gff in the wrong place

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Manasa Ramakrishna

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Sep 21, 2018, 11:10:58 AM9/21/18

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Dear Michael,

I’ve been trying to use CLIPper to analyse some of the iCLIP data from my lab. I have installed it according to instructions on your website in a virtual environment called “peaks”. I have attached the various installation messages to this email and as you can see, it installs just fine and the command “clipper –h” gives me the help guide as expected.

However, when I try to run this on an example BAM file as shown below, I get a value error

“ValueError: /home/mr726/00_Software/peaks/lib/python2.7/site-packages/clipper-0.2.0-py2.7-linux-x86_64.egg/clipper/data/hg19.AS.STRUCTURE.COMPILED.gff does not exist”

I can see that these data are in /home/mr726/00_Software/clipper/build/lib.linux-x86_64-2.7/clipper/data but clearly that’s not where the program is expecting it to be. I might be really stupid here but are you able to tell me if I have done anything grossly wrong which could be causing this error?

Kind regards,

Manasa

(peaks) [mr726@login-e-14 clipper]$ clipper -b ../../lustre/01_iclip/testBAM/wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam -s hg19

Traceback (most recent call last):

File "/home/mr726/00_Software/peaks/bin/clipper", line 11, in <module>

load_entry_point('clipper==0.2.0', 'console_scripts', 'clipper')()

File "/home/mr726/00_Software/peaks/lib/python2.7/site-packages/clipper-0.2.0-py2.7-linux-x86_64.egg/clipper/src/peakfinder.py", line 712, in call_main

File "/home/mr726/00_Software/peaks/lib/python2.7/site-packages/clipper-0.2.0-py2.7-linux-x86_64.egg/clipper/src/peakfinder.py", line 521, in main

File "/home/mr726/00_Software/peaks/lib/python2.7/site-packages/clipper-0.2.0-py2.7-linux-x86_64.egg/clipper/src/peakfinder.py", line 179, in build_transcript_data_gtf_as_structure

File "/home/mr726/00_Software/peaks/lib/python2.7/site-packages/clipper-0.2.0-py2.7-linux-x86_64.egg/clipper/__init__.py", line 23, in data_file

ValueError: /home/mr726/00_Software/peaks/lib/python2.7/site-packages/clipper-0.2.0-py2.7-linux-x86_64.egg/clipper/data/hg19.AS.STRUCTURE.COMPILED.gff does not exist