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CK7 / abawaca

abawaca is a binning program for metagenomics
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A release, or at least a manual? #6

Open bsiranosian opened 6 years ago

bsiranosian commented 6 years ago

Hi, are there any plans for an official release of this algorithm? At least a bare-bones manual/readme would be appreciated. I'd really like to use it on my data.

Thanks!

brymerr921 commented 5 years ago

I was able to run this by taking the following steps. Maybe this will help other users.

  1. Create an empty conda environment. conda create -n abawaca

  2. Install ABAWACA v1.0.7. source activate abawaca; conda install -c shengwei abawaca (v1.0 is available through the bioconda channel)

  3. Install bioperl. conda install -c bioconda perl-bioperl

  4. Clone the ESOM Github repo locally. git clone https://github.com/CK7/esom.git

  5. Change the first line of prepare_esom_files.pl from #!/usr/bin/perl to #!/usr/bin/env perl

  6. Run prepare_esom_files.pl as follows (with the abawaca environment activated). It will be run on all bam files located in /path/to/bam_files_directory. This will generate files called esom.names and esom.lrn. /path/to/prepare_esom_files.pl -sa /path/to/bam_files_directory/ --bam out_dir scaffolds.fasta

  7. Run abawaca. abawaca out_dir/esom.names out_dir/esom.lrn scaffolds.fasta binning_output

Ash1One commented 5 years ago

Hello, @brymerr921 Thank you for your guidance on abawaca. I am in a puzzel about the result that only a dozen bins have been separated and I tried two datasets but it had no change. I guess if the input files were not enough in 6th step, could you give me some advices?

Thanks!

polinanvkv commented 4 years ago

Hello all,

I'm trying to run abawaca as explained by @brymerr921, but it fails at running prepare_esom_files.pl and the output is: 


Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /home/users/pnovikova/perl5/lib/perl5 /mnt/irisgpfs/users/pnovikova/miniconda3/envs/abawaca/lib/site_perl/5.26.2/x86_64-linux-th
read-multi /mnt/irisgpfs/users/pnovikova/miniconda3/envs/abawaca/lib/site_perl/5.26.2 /mnt/irisgpfs/users/pnovikova/miniconda3/envs/abawaca/lib/5.26.2/x86_64-linux-thread-multi /mnt/irisgpfs/users/pnovikova/miniconda3/envs/aba
waca/lib/5.26.2 .) at esom/prepare_esom_files.pl line 4.
BEGIN failed--compilation aborted at esom/prepare_esom_files.pl line 4.

As I understand Bio::SeqIO module is missing but I have no clue how to install it. Any ideas on how to fix it ?

CK7 commented 4 years ago

The missing module is bioperl. You can find installation instructions here: https://bioperl.org/

polinanvkv commented 4 years ago

@CK7 that was wrong because I installed bioperl it as was described. After some digging, the right decision is to install conda install -c bioconda perl-bioperl-core at step 3 instead of conda install -c bioconda perl-bioperl.