Installation

1. $ cd /programinstallers/
2. $ git clone --recursive https://github.com/arq5x/lumpy-sv.git
3. $ cd lumpy-sv
4. $ make
5. Install
   $ mkdir /usr/local/bin/lumpy-sv
6. $ cp -pv bin/* /usr/local/bin/lumpy-sv/

   `bin/lumpy' -> `/usr/local/bin/lumpy-sv/lumpy'
   `bin/lumpyexpress' -> `/usr/local/bin/lumpy-sv/lumpyexpress'
   `bin/lumpyexpress.config' -> `/usr/local/bin/lumpy-sv/lumpyexpress.config'

7. $ cp -pvr scripts/* /usr/local/bin/lumpy-sv/

   ‘scripts/bamkit/LICENSE’ -> ‘/usr/local/bin/lumpy-sv/bamkit/LICENSE’
   ‘scripts/bamkit/bamlibs.py’ -> ‘/usr/local/bin/lumpy-sv/bamkit/bamlibs.py’
   ‘scripts/bamkit/bamheadrg.py’ -> ‘/usr/local/bin/lumpy-sv/bamkit/bamheadrg.py’
   ‘scripts/bamkit/bamcleanheader.py’ -> ‘/usr/local/bin/lumpy-sv/bamkit/bamcleanheader.py’
   ‘scripts/bamkit/.gitignore’ -> ‘/usr/local/bin/lumpy-sv/bamkit/.gitignore’
   ‘scripts/bamkit/bamfilterrg.py’ -> ‘/usr/local/bin/lumpy-sv/bamkit/bamfilterrg.py’
   ‘scripts/bamkit/README.md’ -> ‘/usr/local/bin/lumpy-sv/bamkit/README.md’
   ‘scripts/bamkit/.git’ -> ‘/usr/local/bin/lumpy-sv/bamkit/.git’
   ‘scripts/bamkit/bamgroupreads.py’ -> ‘/usr/local/bin/lumpy-sv/bamkit/bamgroupreads.py’
   ‘scripts/bamkit/bamtofastq.py’ -> ‘/usr/local/bin/lumpy-sv/bamkit/bamtofastq.py’
   ‘scripts/bedpe_sort.py’ -> ‘/usr/local/bin/lumpy-sv/bedpe_sort.py’
   ‘scripts/check_sorting.py’ -> ‘/usr/local/bin/lumpy-sv/check_sorting.py’
   ‘scripts/cnvanator_to_bedpes.py’ -> ‘/usr/local/bin/lumpy-sv/cnvanator_to_bedpes.py’
   ‘scripts/extractSplitReads_BwaMem’ -> ‘/usr/local/bin/lumpy-sv/extractSplitReads_BwaMem’
   ‘scripts/get_coverages.py’ -> ‘/usr/local/bin/lumpy-sv/get_coverages.py’
   ‘scripts/get_exclude_regions.py’ -> ‘/usr/local/bin/lumpy-sv/get_exclude_regions.py’
   ‘scripts/l_bp.py’ -> ‘/usr/local/bin/lumpy-sv/l_bp.py’
   ‘scripts/l_merge.py’ -> ‘/usr/local/bin/lumpy-sv/l_merge.py’
   ‘scripts/l_sort.py’ -> ‘/usr/local/bin/lumpy-sv/l_sort.py’
   ‘scripts/lumpyexpress’ -> ‘/usr/local/bin/lumpy-sv/lumpyexpress’
   ‘scripts/lumpyexpress.config’ -> ‘/usr/local/bin/lumpy-sv/lumpyexpress.config’
   ‘scripts/pairend_distro.py’ -> ‘/usr/local/bin/lumpy-sv/pairend_distro.py’
   ‘scripts/prob_bedpe_to_bedgraph.py’ -> ‘/usr/local/bin/lumpy-sv/prob_bedpe_to_bedgraph.py’
   ‘scripts/run_histo.sh’ -> ‘/usr/local/bin/lumpy-sv/run_histo.sh’
   ‘scripts/split_unmapped_to_fasta.pl’ -> ‘/usr/local/bin/lumpy-sv/split_unmapped_to_fasta.pl’
   ‘scripts/vcfToBedpe’ -> ‘/usr/local/bin/lumpy-sv/vcfToBedpe’

8. $ rm /usr/local/bin/lumpy-sv/bamkit/.git* -rf
9. Note that we have installed the lumpyexpress.config file from the scripts directory, rather than the one from the bin directory.
   They are very different, the scripts version appears more advanced. with version 0.2.13 they are almost the same
10. Add to default PATH
    $ sudo nano /etc/profile
    …
    PATH="$PATH:/usr/local/bin/lumpy-sv"
    …
    
11. Modify /usr/local/bin/lumpy-sv/lumpyexpress.config file
    $ nano /usr/local/bin/lumpy-sv/lumpyexpress.config
    LUMPY_HOME=/usr/local/bin/lumpy-sv
    and remove scripts/ from the last four lines. Resulting file

    #!/bin/bash -e
    
    # general
    LUMPY_HOME=/usr/local/bin/lumpy-sv
    
    LUMPY=`which lumpy || true`
    SAMBLASTER=`which samblaster || true`
    # either sambamba or samtools is required
    SAMBAMBA=`which sambamba || true`
    SAMTOOLS=`which samtools || true`
    
    # python 2.7 or newer, must have pysam, numpy installed
    PYTHON=`which python || true`
    
    # python scripts
    PAIREND_DISTRO=$LUMPY_HOME/pairend_distro.py
    BAMGROUPREADS=$LUMPY_HOME/bamkit/bamgroupreads.py
    BAMFILTERRG=$LUMPY_HOME/bamkit/bamfilterrg.py
    BAMLIBS=$LUMPY_HOME/bamkit/bamlibs.py

12. Cleanup
    $ cd /programinstallers && rm lumpy-sv -rf