Update with significant software releases

[KristinaGagalova]

Current versions and available ones

Major

• RepeatModeller 1.0.11-> 2.0.3

Minor

• RepeatMasker open-4.0.9 -> 4.1.5
• MMseqs 9-d36de -> v14.7e284
• vsearch v2.14.1 -> v2.26.1
• HMMer 3.2.1 -> 3.4
• Blast+ 2.9.0 -> 2.14.1 #dependency
• bedtools 2.28.0 -> v2.31.1
• viennarna 2.4.13 -> 2.6.4
• Decipher 2.14.1 -> v2.30.0
• genometools 1.5.10 -> 1.6.5

Patch version

• t-RNAscan2 2.0.3 -> 2.0.12
• Infernal 1.1.2 -> v1.1.4 (dependency of tRNAscan-SE)
• Arargon 1.2.38 -> v1.2.41
• RepeatScout 1.0.5 -> v1.0.6

No changes

• trf 409 #dependecy
• RECON 1.08 #dependency

GiHub installations

• MITEFINDER https://github.com/screamer/miteFinder.git
• EAhelitron https://github.com/dontkme/EAHelitron.git
• StructureFinder https://github.com/viniciusmaracaja/structRNAfinder.git

Python setup - pip instalations

• SeqRenamer https://github.com/darcyabjones/seqrenamer.git (this has to be updated for the linked dependencies. I am using this forked repo)
• Gffpal https://github.com/darcyabjones/gffpal.git # dependency

Other manual installations

• occultercut 1.1.0 - no changes

Proprietary

Rnammer 1.2 - different container

[KristinaGagalova]

Error in mmseqs, new version input options. Updated as (removed --dont-split-seq-by-len)
https://github.com/KristinaGagalova/pante2/blob/0d9667a91134151c709e1339185e38c5c034ad8a/main.nf#L1433

[KristinaGagalova]

Error in tRNAscan

 tRNAscan-SE       -E       -o "A_fumigatus_A1163_chr1_chr2_trnascan.txt"       -f "A_fumigatus_A1163_chr1_chr2_trnascan_ss.txt"       -s "A_fumigatus_A1163_chr1_chr2_trnascan_iso.txt"       -m "A_fumigatus_A1163_chr1_chr2_trnascan_stats.txt"       -b "A_fumigatus_A1163_chr1_chr2_trnascan.bed"       -a "A_fumigatus_A1163_chr1_chr2_trnascan.fasta"       --forceow       --log trna.log       --thread "1"       "A_fumigatus_A1163_chr1_chr2.fasta"

Command exit status:
  2

Command output:
  (empty)

Command error:
  Unable to open /tmp/.tmpdir.51260915//tscan206255.fpass for writing.  Aborting program.

tmp directory has to be changed from the config file.

UPDATE:
THIS ONLY HAPPENS ON DUG - missing /tmp directory on the HPC system

[KristinaGagalova]

Will address #10 even if won't fix it with the old versions

[KristinaGagalova]

Updates on RepeatModeler (-pa option is not available anymore)
https://github.com/KristinaGagalova/pante2/blob/cef5f787e91e5464752b6524eaffabaf154eb724/main.nf#L1329

[KristinaGagalova]

Bio.Alphabet change - update of the script needed or roll back to another version. More details here

ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

[KristinaGagalova]

Missing library to DECIPHER

Error in library("optparse") : there is no package called ‘optparse’
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
Error in library("optparse") : there is no package called ‘optparse’
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
...

[KristinaGagalova]

Bio.Alphabet depreciated (see before)
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

[KristinaGagalova]

RepeatModeller 2.x.x does not have engine. The command needs to be updated