<commit_before>#!/usr/bin/make -rRsf

SHELL=/bin/bash -o pipefail

#USAGE:
#
#	make
#

MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
CONDAROOT = ${DIR}/software/anaconda/install/
orthopath := $(shell ls ${DIR}/software/OrthoFinder/orthofinder/orthofuser.py 2>/dev/null)
orthufuserversion = $(shell orthofuser.py --help | grep "OrthoFinder version" | awk '{print $$3}')
transrate := $(shell ls ${DIR}/software/orp-transrate/transrate 2>/dev/null)
transabysspath := $(shell which ${DIR}/software/transabyss/transabyss 2>/dev/null)
transabyssversion = $(shell conda ${DIR}/software/anaconda/install/bin/activate orp 2>/dev/null; transabyss --version 2>/dev/null; conda deactivate 2> /dev/null)
diamond_data := $(shell ls ${DIR}/software/diamond/uniprot_sprot.fasta 2>/dev/null)
busco_data := $(shell ls ${DIR}/busco_dbs/eukaryota_odb10 2>/dev/null)
conda := $(shell ${DIR}/software/anaconda/install/bin/conda info 2>/dev/null)
orp := $(shell ${DIR}/software/anaconda/install/bin/conda info --envs | grep orp 2>/dev/null)
VERSION := ${shell cat  ${MAKEDIR}version.txt}

all: setup conda orp orthofuser transrate transabyss diamond_data busco_data postscript

.DELETE_ON_ERROR:

setup:
	@mkdir -p ${DIR}/shared
	@mkdir -p ${DIR}/software/anaconda
	@mkdir -p ${DIR}/software/diamond

conda:setup
ifdef conda
else
	cd ${DIR}/software/anaconda && curl -LO https://repo.anaconda.com/archive/Anaconda3-2019.10-Linux-x86_64.sh
	cd ${DIR}/software/anaconda && bash Anaconda3-2019.10-Linux-x86_64.sh -b -p install/
	echo ". ${DIR}/software/anaconda/install/etc/profile.d/conda.sh" >> ~/.bashrc;
	source ~/.bashrc;
endif

orp:orp_env.yml conda setup
ifdef orp
else
	( \
				source ${DIR}/software/anaconda/install/etc/profile.d/conda.sh; \
				conda activate; \<commit_msg>look for system conda<commit_after>#!/usr/bin/make -rRsf

SHELL=/bin/bash -o pipefail

#USAGE:
#
#	make
#

MAKEDIR := $(dir $(firstword $(MAKEFILE_LIST)))
DIR := ${CURDIR}
CONDAROOT = ${DIR}/software/anaconda/install/
orthopath := $(shell ls ${DIR}/software/OrthoFinder/orthofinder/orthofuser.py 2>/dev/null)
orthufuserversion = $(shell orthofuser.py --help | grep "OrthoFinder version" | awk '{print $$3}')
transrate := $(shell ls ${DIR}/software/orp-transrate/transrate 2>/dev/null)
transabysspath := $(shell which ${DIR}/software/transabyss/transabyss 2>/dev/null)
transabyssversion = $(shell conda ${DIR}/software/anaconda/install/bin/activate orp 2>/dev/null; transabyss --version 2>/dev/null; conda deactivate 2> /dev/null)
diamond_data := $(shell ls ${DIR}/software/diamond/uniprot_sprot.fasta 2>/dev/null)
busco_data := $(shell ls ${DIR}/busco_dbs/eukaryota_odb10 2>/dev/null)
conda := $(shell conda info 2>/dev/null)
orp := $(shell ${DIR}/software/anaconda/install/bin/conda info --envs | grep orp 2>/dev/null)
VERSION := ${shell cat  ${MAKEDIR}version.txt}

all: setup conda orp orthofuser transrate transabyss diamond_data busco_data postscript

.DELETE_ON_ERROR:

setup:
	@mkdir -p ${DIR}/shared
	@mkdir -p ${DIR}/software/anaconda
	@mkdir -p ${DIR}/software/diamond

conda:setup
ifdef conda
else
	cd ${DIR}/software/anaconda && curl -LO https://repo.anaconda.com/archive/Anaconda3-2019.10-Linux-x86_64.sh
	cd ${DIR}/software/anaconda && bash Anaconda3-2019.10-Linux-x86_64.sh -b -p install/
	echo ". ${DIR}/software/anaconda/install/etc/profile.d/conda.sh" >> ~/.bashrc;
	source ~/.bashrc;
endif

orp:orp_env.yml conda setup
ifdef orp
else
	( \
				source ${DIR}/software/anaconda/install/etc/profile.d/conda.sh; \
				conda activate; \
{'fraction_non_alphanumeric': 0.1701162461015027, 'fraction_numerical': 0.019846895378508648, 'mean_word_length': 4.626794258373206, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 27, 'https://': 2, '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': '385858', 'n_tokens_mistral': 1453, 'n_tokens_neox': 1320, 'n_words': 269}