<commit_before>#
# vcr.py
#  - Configures the environment for running the Viral Assembly (vir-assembly-pipeline.sh) and VIGOR (VIGOR3.pl) pipelines (creating directory structure and installs software). 
#

import os.path, re
from fabric.api import cd, env, hide, local, run, settings, sudo, task
from fabric.network import disconnect_all

# Common variables
dependency_URL = "http://s3.amazonaws.com/VIGOR-GSC"

# Viral Assembly
viral_dirs = {}
viral_urls = {}
viral_tars = {}

# GSC Setup - Patches to integrate Viral Assembly and Annotation tools in Galaxy and enabling galaxy to write to /usr/local

def install_GSC_patches(env):
	sudo("wget --no-check-certificate -O /mnt/galaxyTools/galaxy-central/tool_conf.xml.patch %s/tool_conf.xml.patch" % dependency_URL)
	sudo("wget --no-check-certificate -O /mnt/galaxyTools/galaxy-central/tools/viral-assembly-annotation.patch %s/viral-assembly-annotation.patch" % dependency_URL)
	with cd("/mnt/galaxyTools/galaxy-central"):
		sudo("patch tool_conf.xml < tool_conf.xml.patch")
	with cd("/mnt/galaxyTools/galaxy-central/tools"):
		sudo("patch -p1 < viral-assembly-annotation.patch")
	<commit_msg>Renaming install_GSC_patches to install_gsc_patches<commit_after>#
# vcr.py
#  - Configures the environment for running the Viral Assembly (vir-assembly-pipeline.sh) and VIGOR (VIGOR3.pl) pipelines (creating directory structure and installs software). 
#

import os.path, re
from fabric.api import cd, env, hide, local, run, settings, sudo, task
from fabric.network import disconnect_all

# Common variables
dependency_URL = "http://s3.amazonaws.com/VIGOR-GSC"

# Viral Assembly
viral_dirs = {}
viral_urls = {}
viral_tars = {}

# GSC Setup - Patches to integrate Viral Assembly and Annotation tools in Galaxy and enabling galaxy to write to /usr/local

def install_gsc_patches(env):
	sudo("wget --no-check-certificate -O /mnt/galaxyTools/galaxy-central/tool_conf.xml.patch %s/tool_conf.xml.patch" % dependency_URL)
	sudo("wget --no-check-certificate -O /mnt/galaxyTools/galaxy-central/tools/viral-assembly-annotation.patch %s/viral-assembly-annotation.patch" % dependency_URL)
	with cd("/mnt/galaxyTools/galaxy-central"):
		sudo("patch tool_conf.xml < tool_conf.xml.patch")
	with cd("/mnt/galaxyTools/galaxy-central/tools"):
		sudo("patch -p1 < viral-assembly-annotation.patch")
	
{'fraction_non_alphanumeric': 0.12058570198105081, 'fraction_numerical': 0.002583979328165375, 'mean_word_length': 4.926020408163265, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 8}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4515928', 'n_tokens_mistral': 810, 'n_tokens_neox': 777, 'n_words': 185}