Something to add to the README.md #59
Description
I noticed that you have a section about unicycler installation issues (https://github.com/gbouras13/plassembler?tab=readme-ov-file#unicycler-v050-installation-issues), and I thought I would bring something to your attention to help you help users.
Sometimes the output for unicycler --version is as follows:
$ unicycler --version
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
Unicycler v0.5.0This causes plassembler to fail with the following message even though unicycler is installed
2025-02-26 21:48:55.148 | INFO | plassembler:begin_plassembler:100 - You are using Plassembler version 1.6.2
2025-02-26 21:48:55.148 | INFO | plassembler:begin_plassembler:101 - Repository homepage is https://github.com/gbouras13/plassembler
2025-02-26 21:48:55.148 | INFO | plassembler:begin_plassembler:102 - Written by George Bouras: george.bouras@adelaide.edu.au
2025-02-26 21:48:55.148 | INFO | plassembler:run:405 - Database directory is /plassembler_db
2025-02-26 21:48:55.148 | INFO | plassembler:run:406 - Longreads file is plassembler-v1.6.2/test_data/Fastqs/test_long_reads.fastq.gz
2025-02-26 21:48:55.149 | INFO | plassembler:run:407 - R1 fasta file is plassembler-v1.6.2/test_data/Fastqs/test_short_reads_R1.fastq.gz
2025-02-26 21:48:55.149 | INFO | plassembler:run:408 - R2 fasta file is plassembler-v1.6.2/test_data/Fastqs/test_short_reads_R2.fastq.gz
2025-02-26 21:48:55.149 | INFO | plassembler:run:409 - Chromosome length threshold is 50000
2025-02-26 21:48:55.149 | INFO | plassembler:run:410 - Output directory is output_test
2025-02-26 21:48:55.149 | INFO | plassembler:run:411 - Min long read length is 500
2025-02-26 21:48:55.150 | INFO | plassembler:run:412 - Min long read quality is 9
2025-02-26 21:48:55.150 | INFO | plassembler:run:413 - Thread count is 4
2025-02-26 21:48:55.150 | INFO | plassembler:run:414 - --force is False
2025-02-26 21:48:55.150 | INFO | plassembler:run:415 - --skip_qc is False
2025-02-26 21:48:55.150 | INFO | plassembler:run:416 - --raw_flag is False
2025-02-26 21:48:55.150 | INFO | plassembler:run:417 - --pacbio_model is nothing
2025-02-26 21:48:55.151 | INFO | plassembler:run:418 - --keep_fastqs is False
2025-02-26 21:48:55.151 | INFO | plassembler:run:419 - --keep_chromosome is False
2025-02-26 21:48:55.151 | INFO | plassembler:run:420 - --flye_directory is nothing
2025-02-26 21:48:55.151 | INFO | plassembler:run:421 - --flye_assembly is nothing
2025-02-26 21:48:55.151 | INFO | plassembler:run:422 - --flye_info is nothing
2025-02-26 21:48:55.151 | INFO | plassembler:run:423 - --no_chromosome is False
2025-02-26 21:48:55.151 | INFO | plassembler:run:424 - --use_raven is False
2025-02-26 21:48:55.152 | INFO | plassembler:run:425 - --depth_filter is 0.25
2025-02-26 21:48:55.152 | INFO | plassembler:run:426 - --unicycler_options is None
2025-02-26 21:48:55.152 | INFO | plassembler:run:427 - --spades_options is None
2025-02-26 21:48:55.152 | INFO | plassembler:run:431 - Checking dependencies
2025-02-26 21:48:55.225 | INFO | plassembler.utils.input_commands:check_dependencies:199 - Flye version found is v2.9.5-b1801.
2025-02-26 21:48:55.225 | INFO | plassembler.utils.input_commands:check_dependencies:209 - Flye version is ok.
2025-02-26 21:48:55.235 | INFO | plassembler.utils.input_commands:check_dependencies:218 - Raven v1.8.3 found.
2025-02-26 21:48:55.235 | INFO | plassembler.utils.input_commands:check_dependencies:220 - Raven version is ok.
2025-02-26 21:48:55.314 | ERROR | plassembler.utils.input_commands:check_dependencies:239 - Unicycler not found. Please re-install Unicycler, see instructions at https://github.com/gbouras13/plassembler.This issue is resolved by setting TERM in the environment to a value appropriate for the end user's environment.
Something like...
export TERM=xterm-256colorAnd then plassembler works fine.