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paulstothard / cgview_comparison_tool

The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
https://paulstothard.github.io/cgview_comparison_tool/
GNU General Public License v3.0
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Incompatibility with BLAST 2.6.0+ #1

Closed glucksfall closed 4 years ago

glucksfall commented 4 years ago

Hello @paulstothard

I found a problem trying to run scripts/process_test_projects.sh

DESCRIPTION
   Protein Query-Translated Subject BLAST 2.6.0+

Use '-help' to print detailed descriptions of command line arguments
========================================================================

Error: Unknown argument: "query_gencode"
Error:  (CArgException::eInvalidArg) Unknown argument: "query_gencode"
Program failed, try executing the command manually.

Moreover, I have BLAST 2.9.0 that should be the first option and you included BLAST 2.2.26.

Should I use BLAST 2.2.26 to run your software?

Thank you for your time, Best regard.

paulstothard commented 4 years ago

Hello,

Yes unfortunately the CGView Comparison Tool requires the older "legacy" BLAST, so you will need to use BLAST 2.2.26 or one of the older versions. One some platforms it can be difficult to setup legacy BLAST, so for that reason I often use the CCT Docker container.

Paul

glucksfall commented 4 years ago

Thank you for the response.

I will think about a workaround for BLAST because the docker isn't an option to use in our cluster.

Best regard.

paulstothard commented 4 years ago

There may be a suitable binary here (the source is provided too):

https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/

glucksfall commented 4 years ago

Yes, thank you. The problem is I have installed a default version for BLAST, so the user of your software must configure its environment to work with another BLAST version and not interfere with others.

I modified global_settings.conf and set the path to blastall and formatdb with the legacy_blast included in your software. I need to inform the final user how to use the configuration file (or create an alias for the software).

Thank you for all your time.

glucksfall commented 4 years ago

Well... the config file is the default option. No need to scratch my head anymore. Thanks, best regards.