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Shamir-Lab / Recycler

This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir
BSD 3-Clause "New" or "Revised" License
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error creating the BAM file #9

Open Niazevedo opened 7 years ago

Niazevedo commented 7 years ago

Hi I'm trying to create the BAM file and it gives an error. I have installed recycler using bioconda.

This is the error:

Danielas-Mac:Recycler niazevedo$ make_fasta_from_fastg.py -g assembly_graph1.fastg Traceback (most recent call last): File "/Users/niazevedo/anaconda/bin/make_fasta_from_fastg.py", line 4, in import('pkg_resources').run_script('recycler==0.6', 'make_fasta_from_fastg.py') File "/Users/niazevedo/anaconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 744, in run_script File "/Users/niazevedo/anaconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 1506, in run_script File "/Users/niazevedo/anaconda/lib/python2.7/site-packages/recycler-0.6-py2.7.egg/EGG-INFO/scripts/make_fasta_from_fastg.py", line 3, in requires = 'recycler==0.6' File "/Users/niazevedo/anaconda/bin/recycle.py", line 4, in import('pkg_resources').run_script('recycler==0.6', 'recycle.py') File "/Users/niazevedo/anaconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 744, in run_script File "/Users/niazevedo/anaconda/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 1506, in run_script File "/Users/niazevedo/anaconda/lib/python2.7/site-packages/recycler-0.6-py2.7.egg/EGG-INFO/scripts/recycle.py", line 5, in

File "/Users/niazevedo/anaconda/lib/python2.7/site-packages/pysam/init.py", line 5, in from pysam.libchtslib import * ImportError: dlopen(/Users/niazevedo/anaconda/lib/python2.7/site-packages/pysam/libchtslib.so, 2): Library not loaded: @rpath/libhts.1.dylib Referenced from: /Users/niazevedo/anaconda/lib/python2.7/site-packages/pysam/libchtslib.so Reason: image not found

rozovr commented 7 years ago

It looks like an installation problem - have you tried the non-bioconda install steps?