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planemo installation error and new category not recognized #1256

@kenza12

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@kenza12

Hi, I'm trying to reinstall planemo this way but it fails:

root@fc64b8caa435:/galaxy# python3 -m venv planemo
root@fc64b8caa435:/galaxy# . planemo/bin/activate
(planemo) root@fc64b8caa435:/galaxy# pip install -U git+git://github.com/galaxyproject/planemo.git
Collecting git+git://github.com/galaxyproject/planemo.git
  Cloning git://github.com/galaxyproject/planemo.git to /tmp/pip-req-build-x22n7937
fatal: unable to connect to github.com:
github.com[0: 140.82.121.3]: errno=Connection timed out


Command "git clone -q git://github.com/galaxyproject/planemo.git /tmp/pip-req-build-x22n7937" failed with error code 128 in None
You are using pip version 18.1, however version 21.3.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

I also installed it this way: pip install -U planemo. It worked but I don't have the latest updates as you can see here:


(planemo) root@cca0051d1828:/galaxy/toolshed/retropath2# planemo shed_init --name=retropath2 --owner=tduigou --description=DNA assembly using BASIC on OpenTrons --homepage_url=https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT --long_description='Perform retrosynthesis search of possible metabolic routes between a source molecule and a collection of sink molecules. It takes for input the minimal (dmin) and maximal (dmax) diameter for the reaction rules and the maximal path length (maxSteps). The tool expects the following files: rules.csv, sink.csv and source.csv and produce a retrosynthesis network as a CSV file providing reactions in the reaction SMILES format and chemicals in both SMILES and InChI formats along with other information like the score for each reaction.' --category='Synthetic Biology'
Usage: planemo shed_init [OPTIONS] PROJECT
Try 'planemo shed_init --help' for help.

Error: Invalid value for '--category': 'Synthetic Biology' is not one of 'Assembly', 'ChIP-seq', 'Combinatorial Selections', 'Computational chemistry', 'Constructive Solid Geometry', 'Convert Formats', 'Data Export', 'Data Managers', 'Data Source', 'Entomology', 'Epigenetics', 'Fasta Manipulation', 'Fastq Manipulation', 'Flow Cytometry Analysis', 'Genome annotation', 'Genome editing', 'Genome-Wide Association Study', 'Genomic Interval Operations', 'Graphics', 'Imaging', 'Machine Learning', 'Metabolomics', 'Metagenomics', 'Micro-array Analysis', 'Molecular Dynamics', 'Next Gen Mappers', 'NLP', 'Ontology Manipulation', 'Phylogenetics', 'Proteomics', 'RNA', 'SAM', 'Sequence Analysis', 'Statistics', 'Systems Biology', 'Text Manipulation', 'Tool Dependency Packages', 'Tool Generators', 'Transcriptomics', 'Variant Analysis', 'Visualization', 'Web Services'.

Synthetic Biology category was not recognized even if it exists.

I already posted this issue on Gitter: https://gitter.im/galaxy-iuc/iuc

Thank you.

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