<commit_before>#!/usr/bin/env bash
. src/misc.sh

generate_tools_yml $tool_playbook_dir/tools.yml

source $galaxy_dir/.venv/bin/activate

current_dir=$PWD

echo "Populate with tools..."
cd $tool_playbook_dir
ansible-playbook tools.yml -i "localhost,"
cd $current_dir
echo ""


echo "Populate with workflows..."
for i in $( ls $workflow_dir/*.ga )
do
    echo $i
    workflow_path=$workflow_dir"/"$i
    #python ./src/integrate_workflow_in_gi.py \
    #    --workflow_path $i \
    #    --gi_url "http://"$host":"$port \
    #    --api_key $master_api_key
done<commit_msg>Add symlink for samtools<commit_after>#!/usr/bin/env bash
. src/misc.sh

generate_tools_yml $tool_playbook_dir/tools.yml

source $galaxy_dir/.venv/bin/activate

current_dir=$PWD

echo "Populate with tools..."
cd $tool_playbook_dir
ansible-playbook tools.yml -i "localhost,"
cd $current_dir
echo ""


echo "Populate with workflows..."
for i in $( ls $workflow_dir/*.ga )
do
    echo $i
    workflow_path=$workflow_dir"/"$i
    #python ./src/integrate_workflow_in_gi.py \
    #    --workflow_path $i \
    #    --gi_url "http://"$host":"$port \
    #    --api_key $master_api_key
done

declare RESULT=($(python $src_prepare/get_installed_tool_info.py \
    --tool_name "package_samtools_1_2" \
    --tool_shed "toolshed.g2.bx.psu.edu" \
    --gi_url $gi_url \
    --api_key $master_api_key))
revision=${RESULT[0]}
owner=${RESULT[1]}
ln -s $galaxy_dir/dependency_dir/samtools/1.2/$owner/package_samtools_1_2/$revision/bin/samtools $galaxy_dir/.venv/bin/samtools
{'fraction_non_alphanumeric': 0.1497710922171354, 'fraction_numerical': 0.005886200130804447, 'mean_word_length': 3.5808383233532934, 'pattern_counts': {'":': 2, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, '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': '6596428', 'n_tokens_mistral': 616, 'n_tokens_neox': 594, 'n_words': 105}