Closed:How to fix CrossMap tool installation errors and what other tool can do BED2VCF conversion?
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4.1 years ago

How to fix CrossMap tool installation errors and what other tool can do BED2VCF conversion?

After running sudo pip install CrossMap I get:

mat29@mat29-VirtualBox ~ $ pip install CrossMap
Collecting CrossMap
  Using cached CrossMap-0.2.7-py2-none-any.whl
Collecting bx-python (from CrossMap)
  Using cached bx-python-0.8.1.tar.gz
Collecting pysam (from CrossMap)
  Using cached pysam-0.14.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting cython>=0.17 (from CrossMap)
  Using cached Cython-0.28.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting python-lzo (from bx-python->CrossMap)
  Using cached python-lzo-1.11.tar.gz
Collecting numpy (from bx-python->CrossMap)
  Using cached numpy-1.14.2-cp27-cp27mu-manylinux1_x86_64.whl
Requirement already satisfied: six in ./.local/lib/python2.7/site-packages (from bx-python->CrossMap)
Installing collected packages: python-lzo, numpy, bx-python, pysam, cython, CrossMap
  Running setup.py install for python-lzo ... error
    Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-TTnehn/python-lzo/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-b5QMhX-record/install-record.txt --single-version-externally-managed --compile:
    /usr/lib/python2.7/distutils/dist.py:251: UserWarning: 'licence' distribution option is deprecated; use 'license'
      warnings.warn(msg)
    running install
    running build
    running build_ext
    building 'lzo' extension
    creating build
    creating build/temp.linux-x86_64-2.7
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/lzo -I/usr/include/python2.7 -c lzomodule.c -o build/temp.linux-x86_64-2.7/lzomodule.o
    lzomodule.c:35:19: fatal error: lzo1x.h: No such file or directory
    compilation terminated.
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
software error crossmap bed2vcf • 1.2k views
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