PASA release v2.5.3 June 1, 2023

• various bugfixes
• support for singularity added
• set gene_id and model_id to varchar 3000 in mysql schema

** Download the FULL version containing all required submodules **

PASA Release v2.5.2

-bufix and reconfigured CPU propagation to aligners. Each aligner is run individually/sequentially at the full --CPU setting.

** download FULL version for required submodules **

-bugfix - now passing on multithreading parameters to pblat execution

download the FULL version - contains required submodules

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PASA release v2.5.0, Aug 10, 2021

-added minimap2 support
-uses latest gmap software
-uses gmapl for large genomes (bigger than 2^32)
-support for mysql in docker
-using pblat in place of regular blat

PASA release v2.4.1, Nov. 9, 2019

-mysql schema updates for compatibility with latest mysql
-pasaweb updates to leverage user perl @inc environment - finds user installed modules.
-plugin compilation updates for macs
-docker adds pasa binary to /usr/local/bin
-datetime printed for each step of the pipeline execution
-transdecoder updated to current version
-db connection updates for mysql to catch 'lost server'
-including SAM_to_gtf.pl for potential minimap2 integration

Download the FULL version below

bugfix release. If using seqclean for transcript cleaning and for polyA-site identification, this patch release should work for you.

Also updated TransDecoder to latest release v5.2.0
Pipeliner updates to better follow operations

maybe a little more than a bugfix release, but intended to be mostly a bugfix release.

Download the FULL version that comes w/ the submodules populated.

-removed cdbyank from most operations to reduce I/O bound issues w/ large chromosomes.
-updated multithreading around sqlite usage to avoid db locking issues.

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PASA Release v2.3.1 April 12, 2018

-bugfix: if users specified both gmap and blat alignments, only blat was being uploaded. This is unique to v2.3.0 and had to do w/ the new pipeliner and checkpointing system. This is now fixed, and both gmap and blat will be leveraged together as in earlier versions of PASA.

** download the FULL version, which contains required submodules **

-Integration of SQLite (by Nathan Weeks)
-GTF and GFF3 annotation support.
-PasaWeb updates for using SQLite and lighttpd
-upgraded TransDecoder, now including as a submodule
-restructured build process, relocating cdbtools to pasa-plugins
-option --cufflinks_gtf changed to --trans_gtf to be more generic (ie. use stringtie or other)
-docker now supported for PASA
-pipeliner overhauled, now auto-resume integrated.
-added Docker support

bugfix - split genes are now assigned unique gene identifiers.

The env var PASACONF can be used to point PASA towards a user-specific 'conf.txt' file for user-specific mysql login info.