<commit_before>##depends:none

source ../installation_files/functions.bash

# mothur GPLv3
cd ${TMPDIR_PATH}/

# Retain version 1.41.3 as backup
cd ${TMPDIR_PATH}/
wget_retry -nv https://github.com/mothur/mothur/releases/download/v1.41.3/Mothur.linux_64.zip
unzip -q Mothur.linux_64.zip
mv mothur ${TOOLS_PATH}/mothur-1.41.3
rm -rf  __MACOSX
#cd ${TOOLS_PATH}
#ln -s mothur-1.41.3 mothur

# Make version 1.44.3 the default
cd ${TMPDIR_PATH}/
wget_retry -nv https://github.com/mothur/mothur/releases/download/v1.44.3/Mothur.linux.zip
unzip -q Mothur.linux.zip
mv mothur ${TOOLS_PATH}/mothur-1.44.3
rm -rf  __MACOSX
cd ${TOOLS_PATH}
ln -s mothur-1.44.3 mothur

mkdir -p ${TOOLS_PATH}/mothur-silva-reference/
curl -s http://$NIC_MIRROR/pub/sci/molbio/chipster/dist/tools_extras/mothur/silva/v102.tar.lz4  | lz4 -d | tar -x -C ${TOOLS_PATH}/mothur-silva-reference/
curl -s http://$NIC_MIRROR/pub/sci/molbio/chipster/dist/tools_extras/mothur/silva/v132.tar.lz4  | lz4 -d | tar -x -C ${TOOLS_PATH}/mothur-silva-reference/
curl -s http://$NIC_MIRROR/pub/sci/molbio/chipster/dist/tools_extras/mothur/silva/silva-gold.tar.lz4  | lz4 -d | tar -x -C ${TOOLS_PATH}/mothur-silva-reference/

ln -s v132 ${TOOLS_PATH}/mothur-silva-reference/silva

mkdir -p ${TOOLS_PATH}/mothur-unite-reference/
curl -s https://a3s.fi/bundle-builds/mothur-UNITEv8_2020-12-15.tar.lz4  | lz4 -d | tar -x -C ${TOOLS_PATH}/mothur-unite-reference/<commit_msg>Don't use wget_retry<commit_after>##depends:none

# mothur GPLv3
cd ${TMPDIR_PATH}/

# Retain version 1.41.3 as backup
cd ${TMPDIR_PATH}/
wget -nv https://github.com/mothur/mothur/releases/download/v1.41.3/Mothur.linux_64.zip
unzip -q Mothur.linux_64.zip
mv mothur ${TOOLS_PATH}/mothur-1.41.3
rm -rf  __MACOSX
#cd ${TOOLS_PATH}
#ln -s mothur-1.41.3 mothur

# Make version 1.44.3 the default
cd ${TMPDIR_PATH}/
wget -nv https://github.com/mothur/mothur/releases/download/v1.44.3/Mothur.linux.zip
unzip -q Mothur.linux.zip
mv mothur ${TOOLS_PATH}/mothur-1.44.3
rm -rf  __MACOSX
cd ${TOOLS_PATH}
ln -s mothur-1.44.3 mothur

mkdir -p ${TOOLS_PATH}/mothur-silva-reference/
curl -s http://$NIC_MIRROR/pub/sci/molbio/chipster/dist/tools_extras/mothur/silva/v102.tar.lz4  | lz4 -d | tar -x -C ${TOOLS_PATH}/mothur-silva-reference/
curl -s http://$NIC_MIRROR/pub/sci/molbio/chipster/dist/tools_extras/mothur/silva/v132.tar.lz4  | lz4 -d | tar -x -C ${TOOLS_PATH}/mothur-silva-reference/
curl -s http://$NIC_MIRROR/pub/sci/molbio/chipster/dist/tools_extras/mothur/silva/silva-gold.tar.lz4  | lz4 -d | tar -x -C ${TOOLS_PATH}/mothur-silva-reference/

ln -s v132 ${TOOLS_PATH}/mothur-silva-reference/silva

mkdir -p ${TOOLS_PATH}/mothur-unite-reference/
curl -s https://a3s.fi/bundle-builds/mothur-UNITEv8_2020-12-15.tar.lz4  | lz4 -d | tar -x -C ${TOOLS_PATH}/mothur-unite-reference/
{'fraction_non_alphanumeric': 0.164638511095204, 'fraction_numerical': 0.04581245526127416, 'mean_word_length': 3.89492119089317, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 6, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5987475', 'n_tokens_mistral': 1402, 'n_tokens_neox': 1289, 'n_words': 205}