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| #!/usr/bin/env sh | |
| export CPP_INCLUDE_PATH=${CONDA_PREFIX}/include | |
| export CXX_INCLUDE_PATH=${CONDA_PREFIX}/include | |
| export CPLUS_INCLUDE_PATH=${CONDA_PREFIX}/include | |
| export LIBRARY_PATH=${CONDA_PREFIX}/lib | |
| conda install -y htslib libboost wget samtools bcftools bwa minimap2 bowtie2 tqdm parallel trimmomatic | |
| cd /tmp/ | |
| wget https://github.com/dellytools/delly/archive/v0.8.1.tar.gz | |
| tar -xvf v0.8.1.tar.gz | |
| cd delly-0.8.1 | |
| make all | |
| cp ./src/delly ${CONDA_PREFIX}/bin/delly_0.8.1 | |
| echo '#!/bin/sh' > ${CONDA_PREFIX}/bin/delly | |
| echo export DYLD_FALLBACK_LIBRARY_PATH=${CONDA_PREFIX}/lib >> ${CONDA_PREFIX}/bin/delly | |
| chmod 755 ${CONDA_PREFIX}/bin/delly | |
| cd /tmp/ | |
| wget https://github.com/jodyphelan/pathogen-profiler/archive/v1.1.tar.gz | |
| tar -xvf v1.1.tar.gz | |
| cd pathogen-profiler-1.1/ | |
| python setup.py install | |
| cd /tmp/ | |
| wget https://github.com/jodyphelan/TBProfiler/archive/v2.1.tar.gz | |
| tar -xvf v2.1.tar.gz | |
| cd TBProfiler-2.1/ | |
| python setup.py install | |
| cd /tmp/ | |
| mkdir ${CONDA_PREFIX}/share/tbprofiler | |
| tb-profiler update_tbdb | |
| rm -r v0.8.1.tar.gz delly-0.8.1 tbdb TBProfiler-2.1 v2.1.tar.gz v1.1.tar.gz pathogen-profiler-1.1 |
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