v1.5.1

EI Repeat v1.5.1

What's Changed

Fix

• Possible fix for RepeatModeler error: FastaDB::getSubstr - Error index out of bounds! (SeqID=gi|310, offset=1945, length=71 actualSeqLen=1998) at /path/to/repeatmodeler/1.0.11/x86_64/bin/RepeatModeler line 2069. Command exited with non-zero status 25 6c14025

Full Changelog: v1.5.0...v1.5.1

v1.5.0

EI Repeat v1.5.0

What's Changed

Features

• Updated TransposonPSI to conda release version v1.0.0 edd0469
• Updated BEDTools to v2.31.1 0d1ef12

Other changes

• Round up repeat summary stats for easy interpretation 8391f4f
• Removed exclude node list for transposonpsi 766ea82
• Update README.md

Full Changelog: v1.4.1...v1.5.0

v1.4.1

EI Repeat v1.4.1

Bug fixes

• Added seqkit option --only-id to extract only the fasta headers to prevent RepeatMasker failures 0ec3a24

Other changes

• Update transposonpsi hpc_config.json to exclude a few nodes by default 30ea327

Full Changelog: v1.4.0...v1.4.1

v1.4.0

EI Repeat v1.4.0

Features

• Added new pyproject.toml supporting python Poetry 91f394d
• Added script 'merge_repeats' to merge repeats from input GFF3 fccb7e0

Bug fixes

• RepeatMasker does not create an output file '.masked' if it does not mask any bases. Create output file '.masked' for rule RepeatMasker_RepeatModeler if RepeatMasker completes successfully 26587d1

Full Changelog: v1.3.4...v1.4.0

v1.3.4

EI Repeat v1.3.4

Features

• add new script to compute coverage of BED3 from GFF3 a484726
• remove coverageBed to compute stats as it fails with wheat size genome with error 'ERROR: Received illegal bin number 37450 from getBin call. ERROR: Unable to add record to tree.' 80e7999

Bug fixes

• add missing --type match to add_directives_GFF3.py script to add directives 80e7999

Full Changelog: v1.3.3...v1.3.4

v1.3.3

EI Repeat v1.3.3

Features

• add --keep-going option to enable run of independent jobs if a job fails db4d1a0

Full Changelog: v1.3.2...v1.3.3

v1.3.2

EI Repeat v1.3.2

Features

• add new PAP Jira email address 106277e

Full Changelog: v1.3.1...v1.3.2

v1.3.1

EI Repeat v1.3.1

Features

• add script to convert RepeatMasker .out format to RepeatMasker .gff format when RepeatMasker fails to create it 4f6240b, 6a325b7

Full Changelog: v1.3.0...v1.3.1

v1.3.0

EI Repeat v1.3.0

Features

• add new option --exclude_hosts to 'eirepeat run' to exclude specific HPC hosts 74083ef

Breaking change

• update JIRA post to use JIRA Cloud b16219e

Documentation

• Update README.md 0ed9f05
• Update README.md 300672b

Full Changelog: v1.2.0...v1.3.0

eirepeat-1.2.0

EI Repeat v1.2.0

change JIRA notification

• fix: Turn JIRA notification off when JIRA password file not accessible due to [Errno 13] Permission denied

Updated README.md with pipeline workflow

Full Changelog: v1.1.0...v1.2.0