Commit 69255e06 authored by Luis Pedro Coelho's avatar Luis Pedro Coelho

MIN numpy and pandas are necessary too

Mention in README
Check before import
parent 5b908174
......@@ -40,14 +40,14 @@ universe repository before):
If you use [anaconda](https://www.continuum.io/downloads), you can create an
environment with all necessary dependencies using the following commands:
conda create --name metaSNV boost htslib pkg-config
conda create --name metaSNV boost htslib pkg-config numpy pandas
source activate metaSNV
export CFLAGS=-I$CONDA_ENV_PATH/include
export LD_LIBRARY_PATH=$CONDA_ENV_PATH/lib:$LD_LIBRARY_PATH
If you do not have a C++ compiler, anaconda can also install G++:
conda create --name metaSNV boost htslib pkg-config
conda create --name metaSNV boost htslib pkg-config numpy pandas
source activate metaSNV
# Add this command:
conda install gcc
......
#!/usr/bin/env python
import os # interacting with operating system
import sys # interact with system commandline
import time # print current date/time
import argparse # manage command line options and arguments
import os
import sys
import time
import argparse
import glob
import numpy as np
import pandas as pd
try:
import numpy as np
except ImportError:
sys.stderr.write("Numpy is necessary to run postfiltering.\n")
sys.exit(1)
try:
import pandas as pd
except ImportError:
sys.stderr.write("Pandas is necessary to run postfiltering.\n")
sys.exit(1)
basedir = os.path.dirname(os.path.abspath(__file__))
......
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