Commits

Branch selector

 master

User selector

All users

Datepicker

All time

Commit History

Commits on Jan 30, 2025

• replaced with fasta retriever

  brianjohnhaas

  committed
  cc1f8d7

  Copy full SHA for cc1f8d7

Commits on Dec 15, 2023

• ignore comment lines

  brianjohnhaas

  committed
  2728d78

  Copy full SHA for 2728d78

Commits on Jun 1, 2023

• updated version tag to v2.5.3

  brianjohnhaas

  committed
  d5fdc30

  Copy full SHA for d5fdc30

• docker update for release v2.5.3

  brianjohnhaas

  committed
  e45ffc4

  Copy full SHA for e45ffc4

• release v2.5.3

  brianjohnhaas

  committed
  bbe2d8e

  Copy full SHA for bbe2d8e

Commits on May 12, 2023

• add retrieve_gene_via_gff3_index.pl

  brianjohnhaas

  committed
  d0ccbc1

  Copy full SHA for d0ccbc1

Commits on Mar 29, 2023

• updates for singularity

  brianjohnhaas

  committed
  8d79d82

  Copy full SHA for 8d79d82

• add singularity support

  brianjohnhaas

  committed
  a0cf081

  Copy full SHA for a0cf081

Commits on Feb 11, 2023

• update GTF_utils.pm

  brianjohnhaas

  committed
  fd53c7e

  Copy full SHA for fd53c7e

• fastareader mod update

  brianjohnhaas

  committed
  7ca8f93

  Copy full SHA for 7ca8f93

Commits on Jan 31, 2023

• Merge branch 'devel' of github.com:PASApipeline/PASApipeline into devel

  brianjohnhaas

  committed
  1de4577

  Copy full SHA for 1de4577

• in gff3_file_to_bed.pl just print the gene and let the module take care of representing the isoforms too

  brianjohnhaas

  committed
  65d15ed

  Copy full SHA for 65d15ed

Commits on Jan 21, 2023

• Merge branch 'master' of github.com:PASApipeline/pasapipeline into devel

  brianjohnhaas

  committed
  6172725

  Copy full SHA for 6172725

Commits on Jan 15, 2023

• Update README.md

  brianjohnhaas

  authored
  0f44bc9

  Copy full SHA for 0f44bc9

Commits on Jan 5, 2023

• Merge pull request #272 from jorvis/master

  Show description for 0752756
  brianjohnhaas

  authored
  0752756

  Copy full SHA for 0752756

• Removed -K argument I was testing

  jorvis

  committed
  62d15d4

  Copy full SHA for 62d15d4

• Bugfix: genomeDir was getting added twice to the checkpoint file path

  jorvis

  committed
  0100699

  Copy full SHA for 0100699

Commits on Jan 3, 2023

• Merge pull request #271 from jorvis/master

  Show description for 6f5a439
  brianjohnhaas

  authored
  6f5a439

  Copy full SHA for 6f5a439

Commits on Dec 20, 2022

• be clear about --stringent_alignment_overlap and --gene_overlap being mutually exclusive

  brianjohnhaas

  committed
  d5f0473

  Copy full SHA for d5f0473

Commits on Dec 14, 2022

• Added Pipeline class use with checkpoint on the minimap2 run

  jorvis

  committed
  2b1d012

  Copy full SHA for 2b1d012

Commits on Nov 19, 2022

• updating mysql schema for 3k model_id and gene_id varchar

  brianjohnhaas

  committed
  b341f04

  Copy full SHA for b341f04

Commits on Oct 24, 2022

• unlimit the stack size before running slclust to avoid deep recursions blowing the stack

  brianjohnhaas

  committed
  372a0e7

  Copy full SHA for 372a0e7

• during overlap cluster assignment, cap slclust to 100 pairings per transcript, deals with large alignment stacks

  brianjohnhaas

  committed
  56ed468

  Copy full SHA for 56ed468

Commits on Sep 22, 2022

• can now use pasa based on stringtie alone

  brianjohnhaas

  committed
  0033176

  Copy full SHA for 0033176

• cleanme dont remove new runner

  brianjohnhaas

  committed
  f331fc7

  Copy full SHA for f331fc7

• init updates for using stringtie solo

  brianjohnhaas

  committed
  8671331

  Copy full SHA for 8671331

Commits on Jul 7, 2022

• added lighttpd to the docker

  brianjohnhaas

  committed
  ae07456

  Copy full SHA for ae07456

Commits on May 10, 2022

• update

  brianjohnhaas

  committed
  86b9ae8

  Copy full SHA for 86b9ae8

• only Transdecoder.Predict takes the -m arg

  brianjohnhaas

  committed
  041eb15

  Copy full SHA for 041eb15

• add

  brianjohnhaas

  committed
  a831dce

  Copy full SHA for a831dce

Commits on Mar 29, 2022

• docker push to 2.5.2-dev

  brianjohnhaas

  committed
  6eb5de1

  Copy full SHA for 6eb5de1

• conflict resolution

  brianjohnhaas

  committed
  57fa1be

  Copy full SHA for 57fa1be

• prep for test docker

  brianjohnhaas

  committed
  0f84c11

  Copy full SHA for 0f84c11

• require spliced orient to match between FL alignment and derived gene object

  brianjohnhaas

  committed
  1b72bba

  Copy full SHA for 1b72bba

Commits on Feb 17, 2022

• push docker version tag too!

  brianjohnhaas

  committed
  563a330

  Copy full SHA for 563a330

Pagination

Previous

Next