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Microbiome在2018年发表了一篇基于深度学习鉴定抗性基因的工具DeepARG(https://microbiomejournal.biomedcentral.com/track/pdf/10.1186/s40168-018-0401-z?site=microbiomejournal.biomedcentral.com)
按照https://bitbucket.org/gusphdproj/deeparg-ss上的说明,对DeepARG在Linux系统上进行了安装
利用python的pip 进行安装:
1)首先运行 pip install nolearn
成功安装,提示信息为
“Installing collected packages: tabulate, numpy, Lasagne, scipy, six, Theano, gnumpy, gdbn, scikit-learn, joblib, nolearn
Successfully installed Lasagne-0.1 Theano-1.0.1 gdbn-0.1 gnumpy-0.2 joblib-0.11 nolearn-0.6.0 numpy-1.14.1 scikit-learn-0.19.1 scipy-1.0.0 six-1.11.0 tabulate-0.8.2”
2)其次进行测试,python deepARG.py --help
出现如下报错信息:
Exception: Compilation failed (return status=1): /usr/bin/ld: ./libpython3.5m.a(abstract.o): relocation R_X86_64_32S against `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC. ./libpython3.5m.a: could not read symbols: Bad value. collect2: ld returned 1 exit status.
Google到解决方案是python安装时,参数没有设置完全https://github.com/aigamedev/scikit-neuralnetwork/issues/215
于是重新安装python,安装命令
./configure --prefix=./ --enable-shared --build=x86_64-unknown-linux-gnu
make
make install
3)重新运行python deepARG.py --help
出现如下报错信息:
from Theano.tensor.signal import downsample
ImportError: No module named Theano.tensor.signal
Google到解决方案,https://github.com/Theano/Theano/issues/4337
于是修改lasagne/layers/pool.py中的相关代码
4)重新运行python deepARG.py --help
报错提示参数没用对,报错信息是getopt.GetoptError: option --help not recognized
于是修改为python deepARG.py -h
显示如下
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