eead-csic-compbio/chloroplast_assembly_protocol

Minor comments on the installation instructions

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nterhoeven commented

Hi @eead-csic-compbio

we are currently working on a benchmarking of chloroplast assembly tools (see https://github.com/chloroExtractorTeam/benchmark). In this context, I installed your tool on a fresh installation of Ubuntu 18.04.2 and had to install a few additional packages (see below). You might want to add a note about these in your readme.

  • g++
  • make
  • libz-dev
  • libpcre3-dev
  • java

Also, I get an error when running the Example commands with the data in the test directory. The third script ends with

# Velvet could not assembly any contig (test_cp/assembly_pe_kmer47_sample500000/contigs.fa), exit

This is also the case for the MP and the de-novo examples. The HOWTO_brachy.txt tutorial works fine.

Best,

Niklas

eead-csic-compbio commented

Thanks Niklas for the feedback. I have updated the README files. The examples use tiny input files for convenience and that outcome is expected. Instead the brachy example start by downloading real input files and completes the assembly,
Bruno

nterhoeven commented

Thanks a lot 👍

Just as I thought, the velvet issue was caused by the small dataset. Thanks for confirmation.