22 lines
667 B
Bash
Executable File
22 lines
667 B
Bash
Executable File
#!/bin/bash
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set -e
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git clone https://github.com/Oshlack/JAFFA.git &&
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cd JAFFA
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git checkout 24b1c3b
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cp ../subworkflows/JAFFAL/install_linux64.sh .
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./install_linux64.sh
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# JAFFA uses tools.groovy to locate binaries. We modify it as we only need a small subset or they are already
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# included in our env
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# Tools to be compiled from src/
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bin=$(realpath tools/bin)
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echo "//Tools built locally" >> tools.groovy
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declare -a tools=("reformat" "extract_seq_from_fasta" "make_simple_read_table" "process_transcriptome_align_table" "make_3_gene_fusion_table")
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for b in "${tools[@]}"; do
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echo "$b=\"$bin/$b\"" >> tools.groovy
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done
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echo "minimap2=\"minimap2\"" >> tools.groovy
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