root@iZbp10cjxe9c7ip0m4hzhwZ:/bioapp# pip install RseQC
Looking in indexes: http://mirrors.cloud.aliyuncs.com/pypi/simple/
Collecting RseQC
Downloading http://mirrors.cloud.aliyuncs.com/pypi/packages/ad/2d/b522357135fbaebcd34e57183045107b87015155542ff4b84e73f95f69a2/RSeQC-2.6.4-py2-none-any.whl (130kB)
100% |████████████████████████████████| 133kB 15.6MB/s
Requirement already satisfied: cython>=0.17 in /usr/local/lib/python2.7/dist-packages (from RseQC) (0.28.4)
Requirement already satisfied: pysam in /usr/local/lib/python2.7/dist-packages (from RseQC) (0.14.1)
Collecting bx-python (from RseQC)
Downloading http://mirrors.cloud.aliyuncs.com/pypi/packages/74/3e/f19be7f3fb6c6f7d4932050e3dfb1634354c6e896e27d2301ba4df9145e0/bx-python-0.8.1.tar.gz (1.3MB)
100% |████████████████████████████████| 1.3MB 27.4MB/s
Collecting numpy (from RseQC)
Downloading http://mirrors.cloud.aliyuncs.com/pypi/packages/6a/a9/c01a2d5f7b045f508c8cefef3b079fe8c413d05498ca0ae877cffa230564/numpy-1.14.5-cp27-cp27mu-manylinux1_x86_64.whl (12.1MB)
100% |████████████████████████████████| 12.1MB 31.1MB/s
Collecting python-lzo (from bx-python->RseQC)
Downloading http://mirrors.cloud.aliyuncs.com/pypi/packages/af/60/41f17f56c920a956f1d4b9f04f9755c045b2b06b9dd933b33cdd37ab9fd7/python-lzo-1.12.tar.gz
Requirement already satisfied: six in /usr/local/lib/python2.7/dist-packages (from bx-python->RseQC) (1.11.0)
Building wheels for collected packages: bx-python, python-lzo
Running setup.py bdist_wheel for bx-python ... error
Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ZbI2FB/bx-python/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-iavnDe --python-tag cp27:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-install-ZbI2FB/bx-python/setup.py", line 266, in <module>
main()
File "/tmp/pip-install-ZbI2FB/bx-python/setup.py", line 73, in main
raise Exception( "numpy must be installed to build" )
Exception: numpy must be installed to build
----------------------------------------
Failed building wheel for bx-python
Running setup.py clean for bx-python
Running setup.py bdist_wheel for python-lzo ... error
Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ZbI2FB/python-lzo/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-z6DPys --python-tag cp27:
running bdist_wheel
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:35:23: fatal error: lzo/lzo1x.h: No such file or directory
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
Failed building wheel for python-lzo
Running setup.py clean for python-lzo
Failed to build bx-python python-lzo
Installing collected packages: python-lzo, numpy, bx-python, RseQC
Running setup.py install for python-lzo ... error
Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ZbI2FB/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-record-RR2UTz/install-record.txt --single-version-externally-managed --compile:
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:35:23: fatal error: lzo/lzo1x.h: No such file or directory
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ZbI2FB/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-record-RR2UTz/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-install-ZbI2FB/python-lzo/
You are using pip version 10.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
##RSeQC的安装
pip install numpy
在https://omictools.com/bx-python-tool网站下载bx-python-0.8.1.tar.gz
tar -zxvf bx-python-0.8.1.tar.gz
cd bx-python-0.8.1
python setup.py install
cd /bioapp/
sudo apt-get install liblzo2-dev
pip install RSeQC
***************************************
即可成功