linux质控命令,采用RSeQC 对bam 文件进行质控分析时，用inner

谢谢omicsgene大神的回答

我学习了咱们的linux课了，都学了，大讲堂出的课我大部分都有。这个pysam包我也安装了，但还是存在问题。我尽量将我的问题都描述清楚。我用的组学大讲堂的biolinux。

安装pysam结果如下：

x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/tmp/pip_build_manager/pysam/htslib -I/tmp/pip_build_manager/pysam/samtools -I/tmp/pip_build_manager/pysam/samtools/lz4 -I/tmp/pip_build_manager/pysam/bcftools -I/tmp/pip_build_manager/pysam/pysam -I/tmp/pip_build_manager/pysam -I/usr/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-x86_64-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement

pysam/libchtslib.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.

#error Do not use this file, it is the result of a failed Cython compilation.

error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

----------------------------------------

Cleaning up...

Command /usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_manager/pysam/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-l7Jyzv-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /tmp/pip_build_manager/pysam

Storing debug log for failure in /home/manager/.pip/pip.log

运行pip list 结果，里面有RSeQC，但是没有pysam 。这个好像是biolinux里面本来就有的