<commit_before>
JELLYFISH_CODE="jellyfish-2.1.4"
HTSLIB_CODE="htslib.github.Aug182015.tar.gz"

#######################
### Required by Trinity
#######################

FASTOOL_CODE=fstrozzi-Fastool-7c3e034f05
PARAFLY_CODE=parafly-code
TRIMMOMATIC_CODE=Trimmomatic-0.32

trinity_essentials: jellyfish scaffold_iworm_contigs_target fastool_target parafly_target trimmomatic_target samtools

trimmomatic_target:
	ln -sf ${TRIMMOMATIC_CODE} Trimmomatic


samtools:
	tar xvf samtools-0.1.19.tar.bz2
	cd samtools-0.1.19 && $(MAKE) #LIBPATH=-ltinfo
	mv samtools-0.1.19/samtools ./BIN/.

jellyfish:
	tar -zxvf ${JELLYFISH_CODE}.tar.gz && ln -sf ${JELLYFISH_CODE} tmp.jellyfish<commit_msg>turning ltinfo back on for samtools<commit_after>
JELLYFISH_CODE="jellyfish-2.1.4"
HTSLIB_CODE="htslib.github.Aug182015.tar.gz"

#######################
### Required by Trinity
#######################

FASTOOL_CODE=fstrozzi-Fastool-7c3e034f05
PARAFLY_CODE=parafly-code
TRIMMOMATIC_CODE=Trimmomatic-0.32

trinity_essentials: jellyfish scaffold_iworm_contigs_target fastool_target parafly_target trimmomatic_target samtools

trimmomatic_target:
	ln -sf ${TRIMMOMATIC_CODE} Trimmomatic


samtools:
	tar xvf samtools-0.1.19.tar.bz2
	cd samtools-0.1.19 && $(MAKE) LIBPATH=-ltinfo
	mv samtools-0.1.19/samtools ./BIN/.

jellyfish:
	tar -zxvf ${JELLYFISH_CODE}.tar.gz && ln -sf ${JELLYFISH_CODE} tmp.jellyfish
{'fraction_non_alphanumeric': 0.17016654598117306, 'fraction_numerical': 0.04634322954380883, 'mean_word_length': 6.351063829787234, 'pattern_counts': {'":': 0, '<': 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': '7025225', 'n_tokens_mistral': 613, 'n_tokens_neox': 561, 'n_words': 84}