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immcantation / presto

pRESTO is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). pRESTO is a bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
https://presto.readthedocs.io
GNU Affero General Public License v3.0
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AssemblePairs: error: unrecognized arguments: --aligner blastn #48

Closed ssnn-airr closed 7 years ago

ssnn-airr commented 7 years ago

Original report by SL (Bitbucket: st_ph_n, ).

I want to use AssemblePairs reference with the aligner blastn, and a custom database. AssemblePairs is not recognizing the flag for the aligner name, and providing the path to the executable, does not work. Also, --dbexec is unrecognized for makeblastdb.

ssnn-airr commented 7 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

Howdy,

We added blastn support in the development version (v0.5.2.999), which you can install via: pip3 install hg+https://bitbucket.org/kleinstein/presto#default --user

Further instructions are here: http://presto.readthedocs.io/en/latest/install.html#installation

If you install the development version these options will be available. Probably later this week we'll make an official v0.5.3 release with these changes. There'd just a couple things I want to squeeze in before release.

The docs default to the current development version, and not the version currently on PyPI. You can switch the docs to the v0.5.2 docs via the menu in the lower left.

We should really just switch the docs so that the released version is the default to help avoid confusion.

ssnn-airr commented 7 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

Changed the default landing pages for the readthedocs site to the last released version.