Commit e8252b78 authored by eortega's avatar eortega
Browse files

Merge branch 'freq_matrix_overwritten' into 'master'

Added installer for virtual env

See merge request !2
parents 0a8d8e8b 7ad56d05
#!/bin/bash
## VARIABLES
## Directory containing the virtual environment
py_env_dir=~/envs/coev
## url for the desired python3 executable
py_version=$(readlink $(command -v python3))
echo 'Environment to be installed in: ' $py_env_dir
echo 'Version of python to be used: ' $py_version
## SCRIPT
mkdir -p $py_env_dir
virtualenv -p $py_version $py_env_dir
## INSTALL PACKAGES
# Activate environment
source ${py_env_dir}/bin/activate
# Update pip if necessary
pip install --upgrade pip
##
pip install -r requirements_py-env.txt
# pip install biopython pandas matplotlib multiqc pyvcf
deactivate
......@@ -2,11 +2,14 @@
## PATH TO WORKING DIRECTORY
path=/home/enrique/work/Gandon/coevolution/phages/
path=$1
#path=/home/enrique/work/Gandon/coevolution/phages/
## START ENVIRONMENT TO EXECUTE MULTIQC
source /home/enrique/envs/biopython/bin/activate
source ~/envs/coev/bin/activate
## SEPARATE THE FILES BY NAME
......
......@@ -16,7 +16,8 @@ def run_on_multiple_files(path_to_vcfs, outpath, list_files, list_headers, group
ctrl_file = '/mnt/alpha_raid/work/Gandon/coevolution/phages/results/snpcalling/Other_seq/TO-WT_S83.vcf'
#ctrl_file = '/mnt/alpha_raid/work/Gandon/coevolution/phages/results/snpcalling/Other_seq/TO-WT_S83.vcf'
ctrl_file='/mnt/alpha_raid/work/Gandon/coevolution/phages/steps/snpcalling/Other_seq/TO-WT_S83.vcf'
control = ImportControl2()
......@@ -25,7 +26,7 @@ control.load_vcf(ctrl_file)
path_to_vcfs = '/mnt/alpha_raid/work/Gandon/coevolution/phages/results/snpcalling/W_seq/'
path_to_vcfs = '/mnt/alpha_raid/work/Gandon/coevolution/phages/steps/snpcalling/W_seq/'
outpath = '/mnt/alpha_raid/work/Gandon/coevolution/phages/plots/freq_heatmap/W_seq/'
......
biopython==1.76
certifi==2019.11.28
chardet==3.0.4
Click==7.0
coloredlogs==10.0
colormath==3.0.0
cycler==0.10.0
decorator==4.4.1
future==0.18.2
humanfriendly==4.18
idna==2.8
Jinja2==2.10.3
kiwisolver==1.1.0
lzstring==1.0.4
Markdown==3.1.1
MarkupSafe==1.1.1
matplotlib==2.2.4
multiqc==1.8
networkx==2.2
numpy==1.18.1
pandas==0.24.2
pyparsing==2.4.6
python-dateutil==2.8.1
pytz==2019.3
PyVCF==0.6.8
PyYAML==5.3
requests==2.22.0
simplejson==3.17.0
six==1.13.0
spectra==0.0.11
urllib3==1.25.7
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