<commit_before>#!/bin/bash
set -ex
#bwa
git clone https://github.com/lh3/bwa.git
cd bwa; make
ln -sf $PWD/bwa $HOME/bin/
#bamtools
git clone <EMAIL>:pezmaster31/bamtools.git
cd bamtools
mkdir build
cd build
cmake ..
make
cd ..
ln -sf $PWD/bin/bamtools ~/bin/
#samtools
#bedtools
#seqtk
git clone https://github.com/lh3/seqtk.git;
cd seqtk; make
ln -s $PWD/seqtk $HOME/bin
cd ..
#freebayes
#tabix
git clone <EMAIL>:samtools/tabix.git
cd tabix/
make
ln -s $PWD/tabix ~/bin/
ln -s $PWD/bgzip ~/bin/



#ngmlr, make sure to have at least gcc 5.3
git clone https://github.com/philres/ngmlr.git
pushd ngmlr
mkdir build
pushd build
cmake ..
#modify LIBRARY_PATH as necessary because the compiler looks for static libraries (lib*.a) during compilation
#changing LD_LIBRARY_PATH does not help as it is used for shared libraries (after compilation is done)
make -j
#cmake does not seem to have good support for make -j
make
ln -s $PWD/
popd
popd
<commit_msg>https->ssh<commit_after>#!/bin/bash
set -ex
#bwa
git clone https://github.com/lh3/bwa.git
cd bwa; make
ln -sf $PWD/bwa $HOME/bin/
#bamtools
git clone <EMAIL>:pezmaster31/bamtools.git
cd bamtools
mkdir build
cd build
cmake ..
make
cd ..
ln -sf $PWD/bin/bamtools ~/bin/
#samtools
#bedtools
#seqtk
git clone <EMAIL>:lh3/seqtk.git
cd seqtk; make
ln -s $PWD/seqtk $HOME/bin
cd ..
#freebayes
#tabix
git clone <EMAIL>:samtools/tabix.git
cd tabix/
make
ln -s $PWD/tabix ~/bin/
ln -s $PWD/bgzip ~/bin/



#ngmlr, make sure to have at least gcc 5.3
git clone https://github.com/philres/ngmlr.git
pushd ngmlr
mkdir build
pushd build
cmake ..
#modify LIBRARY_PATH as necessary because the compiler looks for static libraries (lib*.a) during compilation
#changing LD_LIBRARY_PATH does not help as it is used for shared libraries (after compilation is done)
make -j
#cmake does not seem to have good support for make -j
make
ln -s $PWD/
popd
popd

{'fraction_non_alphanumeric': 0.1111111111111111, 'fraction_numerical': 0.006379585326953748, 'mean_word_length': 3.825641025641026, 'pattern_counts': {'":': 0, '<': 8, '<?xml version=': 0, '>': 9, 'https://': 5, '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': '2861656', 'n_tokens_mistral': 759, 'n_tokens_neox': 731, 'n_words': 258}