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Paul Igor Costea
metaSNV
Commits
69255e06
Commit
69255e06
authored
7 years ago
by
Luis Pedro Coelho
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MIN numpy and pandas are necessary too
Mention in README Check before import
parent
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README.md
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README.md
metaSNV_post.py
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-6
14 additions, 6 deletions
metaSNV_post.py
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and
8 deletions
README.md
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69255e06
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@@ -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
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metaSNV_post.py
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14
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69255e06
#!/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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