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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,30 +1,57 @@ | ||
| .PHONY: all data tools pandoc clean | ||
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| all: readme | ||
| data: genome/chrX.fa | ||
| tools: github-markdown-toc samtools pandoc bwa minimap2 | ||
| tools: github-markdown-toc samtools bwa minimap2 mosdepth pandoc | ||
| pandoc: /usr/bin/pandoc | ||
| samtools_ver = 1.18 | ||
| minimap2_ver = 2.24 | ||
| samtools_ver := 1.19.2 | ||
| minimap2_ver := 2.24 | ||
| mosdepth_ver := 0.3.7 | ||
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| genome/chrX.fa: | ||
| bunzip2 -c eg/chrX.fa.bz2 > genome/chrX.fa | ||
| bunzip2 -c eg/chrX.fa.bz2 > $@ | ||
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| github-markdown-toc: | ||
| git clone https://github.com/ekalinin/github-markdown-toc.git | ||
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| samtools: | ||
| wget --quiet https://github.com/samtools/samtools/releases/download/$(samtools_ver)/samtools-$(samtools_ver).tar.bz2 && tar xjf samtools-$(samtools_ver).tar.bz2 && cd samtools-$(samtools_ver) && ./configure && make && mv samtools .. && cd .. && rm -rf samtools-$(samtools_ver).tar.bz2 samtools-$(samtools_ver) | ||
| wget --quiet https://github.com/samtools/samtools/releases/download/$(samtools_ver)/samtools-$(samtools_ver).tar.bz2 \ | ||
| && tar xjf samtools-$(samtools_ver).tar.bz2 \ | ||
| && cd samtools-$(samtools_ver) \ | ||
| && ./configure \ | ||
| && make \ | ||
| && mv samtools .. \ | ||
| && cd .. \ | ||
| && rm -rf samtools-$(samtools_ver).tar.bz2 samtools-$(samtools_ver) | ||
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| bwa: | ||
| wget --quiet https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2 && tar xjf bwa-0.7.17.tar.bz2 && cd bwa-0.7.17 && make && mv bwa .. && cd .. && rm -rf bwa-* | ||
| wget --quiet https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2 \ | ||
| && tar xjf bwa-0.7.17.tar.bz2 \ | ||
| && cd bwa-0.7.17 \ | ||
| && make \ | ||
| && mv bwa .. \ | ||
| && cd .. \ | ||
| && rm -rf bwa-* | ||
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| minimap2: | ||
| wget --quiet https://github.com/lh3/minimap2/archive/refs/tags/v$(minimap2_ver).tar.gz && tar xzf v$(minimap2_ver).tar.gz && cd minimap2-$(minimap2_ver) && make && mv minimap2 .. && cd .. && rm -rf minimap2-* v$(minimap2_ver).tar.gz | ||
| wget --quiet https://github.com/lh3/minimap2/archive/refs/tags/v$(minimap2_ver).tar.gz \ | ||
| && tar xzf v$(minimap2_ver).tar.gz \ | ||
| && cd minimap2-$(minimap2_ver) \ | ||
| && make \ | ||
| && mv minimap2 .. \ | ||
| && cd .. \ | ||
| && rm -rf minimap2-* v$(minimap2_ver).tar.gz | ||
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| mosdepth: | ||
| wget --quiet https://github.com/brentp/mosdepth/releases/download/v$(mosdepth_ver)/mosdepth \ | ||
| && chmod 755 mosdepth | ||
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| /usr/bin/pandoc: | ||
| apt update && apt install -y pandoc | ||
| apt update \ | ||
| && apt install -y pandoc | ||
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| readme: data tools | ||
| ./create_readme.sh | ||
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| clean: | ||
| rm -rf genome/chrX.fa github-markdown-toc samtools tmp.html && eg/clean.sh | ||
| rm -rf genome/chrX.fa github-markdown-toc samtools bwa minimap2 mostdepth tmp.html && eg/clean.sh |