<commit_before>
##Install HapMap2 Panel
wget https://imputationserver.sph.umich.edu/static/downloads/hapmap.tar.gz -O /opt/cloudgene/tmp/hapmap.tar.gz
cd /opt/cloudgene/tmp; tar xvfz hapmap.tar.gz
sudo -u cloudgene hadoop fs -mkdir ref-panels
sudo -u cloudgene hadoop fs -mkdir ref-panels/hapmap_r22.eagle
sudo -u cloudgene hadoop fs -put /opt/cloudgene/tmp/bcfs/*.bcf* ref-panels/hapmap_r22.eagle/.
sudo -u cloudgene hadoop fs -put /opt/cloudgene/tmp/panel/hapmap_r22.CEU.hg19.tgz  ref-panels/.
sudo -u cloudgene hadoop fs -put /opt/cloudgene/tmp/panel/hapmap_r22.CEU.hg19.legends.tgz  ref-panels/.
sudo -u cloudgene hadoop fs -put /opt/cloudgene/tmp/map/genetic_map_hg19_withX.txt.gz  ref-panels/.

# Delete local files
rm -rf /opt/cloudgene/tmp/*

## Connect Imputation Server with Cloudgene
sudo cp /opt/cloudgene/applications/imputationserver/files/config/settings.yaml -R /opt/cloudgene/config/settings.yaml
cp -R /opt/cloudgene/applications/imputationserver/target/minimac-cloud-assembly/minimac /opt/cloudgene/apps/.<commit_msg>setting pages<commit_after>
##Install HapMap2 Panel
wget https://imputationserver.sph.umich.edu/static/downloads/hapmap.tar.gz -O /opt/cloudgene/tmp/hapmap.tar.gz
cd /opt/cloudgene/tmp; tar xvfz hapmap.tar.gz
sudo -u cloudgene hadoop fs -mkdir ref-panels
sudo -u cloudgene hadoop fs -mkdir ref-panels/hapmap_r22.eagle
sudo -u cloudgene hadoop fs -put /opt/cloudgene/tmp/bcfs/*.bcf* ref-panels/hapmap_r22.eagle/.
sudo -u cloudgene hadoop fs -put /opt/cloudgene/tmp/panel/hapmap_r22.CEU.hg19.tgz  ref-panels/.
sudo -u cloudgene hadoop fs -put /opt/cloudgene/tmp/panel/hapmap_r22.CEU.hg19.legends.tgz  ref-panels/.
sudo -u cloudgene hadoop fs -put /opt/cloudgene/tmp/map/genetic_map_hg19_withX.txt.gz  ref-panels/.

# Delete local files
rm -rf /opt/cloudgene/tmp/*

## Connect Imputation Server with Cloudgene
sudo cp /opt/cloudgene/applications/imputationserver/files/config/settings.yaml -R /opt/cloudgene/config/settings.yaml
cp -R /opt/cloudgene/applications/imputationserver/target/minimac-cloud-assembly/minimac /opt/cloudgene/apps/.
cp -R /opt/cloudgene/applications/imputationserver/target/minimac-cloud-assembly/pages /opt/cloudgene/.
{'fraction_non_alphanumeric': 0.125, 'fraction_numerical': 0.013786764705882353, 'mean_word_length': 4.158767772511848, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '877866', 'n_tokens_mistral': 909, 'n_tokens_neox': 826, 'n_words': 162}