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====== FALCON-Phase ======

FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds.

===== Information =====

  * Version: git-7c50154e
  * Added: November, 2020
  * Link: https://github.com/phasegenomics/FALCON-Phase

===== Usage =====

See which versions of falcon-phase are available:
<code>$ module avail falcon-phase</code>

Load one version into your environment:
<code>$ module load falcon-phase/git-7c50154e</code>

//Note:// you need to copy and customize the example ''config.sh'' and ''config.json'' into your working directory. You will need to change the CPU parameters to match the number requested in your SLURM job as well as the paths to your data. I **strongly** recommend running this from the scratch directory on a compute node.

Consult the README for more information: https://github.com/phasegenomics/FALCON-Phase

===== Installation ======

Notes from the sysadmin during installation:

<code>$ cd /tmp
$ git clone --recursive https://github.com/phasegenomics/FALCON-Phase.git
$ cd FALCON-Phase/src
$ make
$ cd ..
$ sudo mkdir -p /export/apps/falcon-phase/git-7c50154e
$ sudo chown aorth:aorth /export/apps/falcon-phase/git-7c50154e
# modify configs for local environment
$ vim pipeline/config.sh
$ vim pipeline/config.json
$ cp -r bin LICENSE.txt pipeline README.md test_data tests validation /export/apps/falcon-phase/git-7c50154e
$ python3 -m venv /export/apps/falcon-phase/git-7c50154e/venv
$ source /export/apps/falcon-phase/git-7c50154e/venv/bin/activate
$ pip install numpy==1.14.2 biopython
$ sudo chmod +x /export/apps/falcon-phase/git-7c50154e/bin/preprocess_diploid_asm_for_fc_phase.py
$ sudo chown -R root:root /export/apps/falcon-phase/git-7c50154e</code>

Test the installation with the included test data:

<code>$ interactive -c 8 -J falcon-PHASE
$ mkdir -p /var/scratch/aorth/2020-11-11-falcon-phase-test
$ cd /var/scratch/aorth/2020-11-11-falcon-phase-test
$ cp -r /export/apps/falcon-phase/git-7c50154e/pipeline/* .
# edit configs!!!
$ module load falcon-phase/git-7c50154e
$ preprocess_diploid_asm_for_fc_phase.py -P /export/apps/falcon-phase/git-7c50154e/test_data/cns_p_ctg.fasta -H /export/apps/falcon-phase/git-7c50154e/test_data/cns_h_ctg.fasta -o cleaned_contigs
$ snakemake -s snakefile --verbose -p</code>