blahah / transrate

Understand your transcriptome assembly
http://hibberdlab.com/transrate
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Linux binary for v1.0.3 cannot be downloaded #253

Open fran-romero-campero opened 7 months ago

fran-romero-campero commented 7 months ago

I have tried to download the binary for linux v1.0.3 but the link seems to be broken.

taein98 commented 6 months ago

I also want to get this.

IBEXCluster commented 6 months ago

dear @fran-romero-campero and @taein98 Conda repository works for me! conda install bioconda::transrate

Note: Please ensure to create Python 3.8.0 virtual environment to address couple of dependencies.

Example:

conda create -n transrate python=3.8.0 source activate transrate conda install bioconda::transrate

$ transrate --help
[DEPRECATION] The trollop gem has been renamed to optimist and will no longer be supported. Please switch to optimist as soon as possible.

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Transrate v1.0.3
by Richard Smith-Unna, Chris Boursnell, Rob Patro,
Julian Hibberd, and Steve Kelly

DESCRIPTION:
Analyse a de-novo transcriptome assembly using three kinds of metrics:

  1. sequence based (if --assembly is given)
  2. read mapping based (if --left and --right are given)
  3. reference based (if --reference is given)

Documentation at http://hibberdlab.com/transrate

USAGE:
transrate

OPTIONS:
--assembly= Assembly file(s) in FASTA format, comma-separated
--left= Left reads file(s) in FASTQ format, comma-separated
--right= Right reads file(s) in FASTQ format, comma-separated
--reference= Reference proteome or transcriptome file in FASTA format
--threads= Number of threads to use (default: 8)
--merge-assemblies= Merge best contigs from multiple assemblies into file
--output= Directory where results are output (will be created) (default: transrate_results)
--loglevel= Log level. One of [error, info, warn, debug] (default: info)
--install-deps= Install any missing dependencies. One of [read, ref, all]
--examples Show some example commands with explanations