This page was last updated on Thursday, 11-May-2017 11:11:12 CDT

Installation notes for Organelle_PBA version 848c3ce on Oct 10, 2016

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Prerequisites

• $ sudo cpan Bio::Tools::Run::StandAloneBlastPlus
  (I had to add -f to force installation)

Installation

1. $ cd /programinstallers/
2. $ cd /usr/local/bin
3. $ git clone https://github.com/aubombarely/Organelle_PBA.git
4. Add to default PATH
   $ sudo nano /etc/profile
   …
   PATH="$PATH:/usr/local/bin/Organelle_PBA"
   …
5. Test
   $ mkdir testrun
6. $ zcat /usr/local/bin/Organelle_PBA/testdata/artha_chl/artha_refchl01_artha.fa.gz > testrun/artha_refchl01_artha.fa
7. $ zcat /usr/local/bin/Organelle_PBA/testdata/artha_chl/artha_pacbioSRR1284093_c025k.fastq.gz > testrun/artha_pacbioSRR1284093_c025k.fastq
8. $ OrganelleRef_PBA -i testrun/artha_pacbioSRR1284093_c025k.fastq -r testrun/artha_refchl01_artha.fa -o testrun -b '-nproc=28' -s 'num_threads=28' >& test.log