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Updated the bcftools and htslib from 1.19 to 1.20
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maurya-anand committed Oct 17, 2024
1 parent ef6b675 commit e38dbde
Showing 1 changed file with 7 additions and 7 deletions.
14 changes: 7 additions & 7 deletions Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -35,18 +35,18 @@ $(SRC_DIR)/genomes/hg19ToHg38.over.chain.gz:
$(SRC_DIR)/tools/libexec/bcftools/liftover.so:
@printf "Installing liftover\n"
@mkdir -p $(SRC_DIR)/tools
@wget --no-check-certificate --no-verbose https://github.com/samtools/bcftools/releases/download/1.19/bcftools-1.19.tar.bz2 -O $(SRC_DIR)/tools/bcftools-1.19.tar.bz2
@tar -xjf $(SRC_DIR)/tools/bcftools-1.19.tar.bz2 -C $(SRC_DIR)/tools
@cd $(SRC_DIR)/tools/bcftools-1.19 && ./configure --prefix=$(SRC_DIR)/tools && make && make install
@wget --no-check-certificate --no-verbose https://github.com/samtools/bcftools/releases/download/1.20/bcftools-1.20.tar.bz2 -O $(SRC_DIR)/tools/bcftools-1.20.tar.bz2
@tar -xjf $(SRC_DIR)/tools/bcftools-1.20.tar.bz2 -C $(SRC_DIR)/tools
@cd $(SRC_DIR)/tools/bcftools-1.20 && ./configure --prefix=$(SRC_DIR)/tools && make && make install

@wget --no-check-certificate --no-verbose https://software.broadinstitute.org/software/score/score_1.20-20240927.zip -O $(SRC_DIR)/tools/score_1.20-20240927.zip
@unzip $(SRC_DIR)/tools/score_1.20-20240927.zip -d $(SRC_DIR)/tools/libexec/bcftools

@wget --no-check-certificate --no-verbose https://github.com/samtools/htslib/releases/download/1.19.1/htslib-1.19.1.tar.bz2 -O $(SRC_DIR)/tools/htslib-1.19.1.tar.bz2
@tar -xjf $(SRC_DIR)/tools/htslib-1.19.1.tar.bz2 -C $(SRC_DIR)/tools
@cd $(SRC_DIR)/tools/htslib-1.19.1 && ./configure --prefix=$(SRC_DIR)/tools && make && make install
@wget --no-check-certificate --no-verbose https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2 -O $(SRC_DIR)/tools/htslib-1.20.tar.bz2
@tar -xjf $(SRC_DIR)/tools/htslib-1.20.tar.bz2 -C $(SRC_DIR)/tools
@cd $(SRC_DIR)/tools/htslib-1.20 && ./configure --prefix=$(SRC_DIR)/tools && make && make install

@rm -rf $(SRC_DIR)/tools/bcftools-1.19.tar.bz2 $(SRC_DIR)/tools/score_1.20-20240927.zip $(SRC_DIR)/tools/bcftools-1.19 $(SRC_DIR)/tools/htslib-1.19.1.tar.bz2 $(SRC_DIR)/tools/htslib-1.19.1
@rm -rf $(SRC_DIR)/tools/bcftools-1.20.tar.bz2 $(SRC_DIR)/tools/bcftools-1.20 $(SRC_DIR)/tools/score_1.20-20240927.zip $(SRC_DIR)/tools/htslib-1.20.tar.bz2 $(SRC_DIR)/tools/htslib-1.20

SCRIPT_DIR := $(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
REFERENCE := $(SRC_DIR)/genomes
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