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galaxyproject / planemo

Command-line utilities to assist in developing Galaxy and Common Workflow Language artifacts - including tools, workflows, and training materials.
https://planemo.readthedocs.io/
MIT License
90 stars 86 forks source link

planemo installation error and new category not recognized #1256

Closed kenza12 closed 2 years ago

kenza12 commented 2 years ago

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.

simonbray commented 2 years ago

Hi @kenza12, what about

pip install -U git+https://github.com/galaxyproject/planemo.git

?

kenza12 commented 2 years ago

pip install -U git+https://github.com/galaxyproject/planemo.git

Hi @simonbray , I don't have the timeout error anymore but I got another error about bioblend:

root@cca0051d1828:/galaxy# python3 -m venv planemo
root@cca0051d1828:/galaxy# . planemo/bin/activate
(planemo) root@cca0051d1828:/galaxy# pip install -U git+https://github.com/galaxyproject/planemo.git
Collecting git+https://github.com/galaxyproject/planemo.git
  Cloning https://github.com/galaxyproject/planemo.git to /tmp/pip-req-build-txr2fqho
  Installing build dependencies ... done
Collecting allure-python-commons (from planemo==0.74.11)
  Downloading https://files.pythonhosted.org/packages/85/39/b85c3c5ba41d40b6b516a9c404e916e50b730071b7daf1c50795eebcc8b8/allure_python_commons-2.9.45-py3-none-any.whl
Collecting bioblend>=0.17.0 (from planemo==0.74.11)
  Could not find a version that satisfies the requirement bioblend>=0.17.0 (from planemo==0.74.11) (from versions: 0.2.1, 0.2.2, 0.2.3, 0.2.4, 0.3.0, 0.3.1, 0.3.2, 0.3.3, 0.4.0, 0.4.1, 0.4.2, 0.4.3, 0.5.0, 0.5.1, 0.5.2, 0.5.3, 0.6.0, 0.6.1, 0.7.0, 0.8.0, 0.9.0, 0.10.0, 0.11.0, 0.12.0, 0.13.0, 0.14.0, 0.15.0, 0.16.0)
No matching distribution found for bioblend>=0.17.0 (from planemo==0.74.11)
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.

(planemo) root@cca0051d1828:/galaxy# pip install --upgrade pip
Collecting pip
  Downloading https://files.pythonhosted.org/packages/a4/6d/6463d49a933f547439d6b5b98b46af8742cc03ae83543e4d7688c2420f8b/pip-21.3.1-py3-none-any.whl (1.7MB)
    100% |████████████████████████████████| 1.7MB 27.0MB/s 
Installing collected packages: pip
  Found existing installation: pip 18.1
    Uninstalling pip-18.1:
      Successfully uninstalled pip-18.1
Successfully installed pip-21.3.1

(planemo) root@cca0051d1828:/galaxy# pip install -U git+https://github.com/galaxyproject/planemo.git
Collecting git+https://github.com/galaxyproject/planemo.git
  Cloning https://github.com/galaxyproject/planemo.git to /tmp/pip-req-build-owtj5zdu
  Running command git clone --filter=blob:none -q https://github.com/galaxyproject/planemo.git /tmp/pip-req-build-owtj5zdu
  Resolved https://github.com/galaxyproject/planemo.git to commit 293c93ccab52d536c8baf6b9beedd8fa631d32f8
  Running command git submodule update --init --recursive -q
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting virtualenv
  Downloading virtualenv-20.15.1-py2.py3-none-any.whl (10.1 MB)
     |████████████████████████████████| 10.1 MB 24.0 MB/s            
Collecting galaxy-containers<22.01
  Downloading galaxy_containers-21.9.0-py2.py3-none-any.whl (28 kB)
Collecting click!=8.0.2
  Downloading click-8.0.4-py3-none-any.whl (97 kB)
     |████████████████████████████████| 97 kB 6.9 MB/s             
Collecting pyyaml
  Downloading PyYAML-6.0-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (603 kB)
     |████████████████████████████████| 603 kB 97.0 MB/s            
Collecting oyaml
  Downloading oyaml-1.0-py2.py3-none-any.whl (3.0 kB)
Collecting galaxy-util<22.01,>=20.5.0
  Downloading galaxy_util-21.9.0-py2.py3-none-any.whl (125 kB)
     |████████████████████████████████| 125 kB 80.2 MB/s            
Collecting glob2
  Downloading glob2-0.7.tar.gz (10 kB)
  Preparing metadata (setup.py) ... done
Collecting galaxy-tool-util<22.01,>=21.1.0.dev4
  Downloading galaxy_tool_util-21.9.2-py2.py3-none-any.whl (328 kB)
     |████████████████████████████████| 328 kB 40.3 MB/s            
Collecting lxml
  Downloading lxml-4.9.1-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (6.4 MB)
     |████████████████████████████████| 6.4 MB 96.1 MB/s            
Collecting jinja2
  Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB)
     |████████████████████████████████| 133 kB 91.9 MB/s            
Collecting tabulate
  Downloading tabulate-0.8.10-py3-none-any.whl (29 kB)
Collecting allure-python-commons
  Using cached allure_python_commons-2.9.45-py3-none-any.whl (15 kB)
ERROR: Could not find a version that satisfies the requirement bioblend>=0.17.0 (from planemo) (from versions: 0.2.1, 0.2.2, 0.2.3, 0.2.4, 0.3.0, 0.3.1, 0.3.2, 0.3.3, 0.4.0, 0.4.1, 0.4.2, 0.4.3, 0.5.0, 0.5.1, 0.5.2, 0.5.3, 0.6.0, 0.6.1, 0.7.0, 0.8.0, 0.9.0, 0.10.0, 0.11.0, 0.12.0, 0.13.0, 0.14.0, 0.15.0, 0.16.0)
ERROR: No matching distribution found for bioblend>=0.17.0
simonbray commented 2 years ago

That is strange, BioBlend version 0.17.0 definitely exists: https://pypi.org/project/bioblend/#history

The following works fine for me, are you doing something different?

virtualenv -p python3.7 test
source test/bin/activate
pip install -U git+https://github.com/galaxyproject/planemo.git
planemo --help
kenza12 commented 2 years ago

I was using planemo documentation: https://planemo.readthedocs.io/en/latest/installation.html

I just figured out that it was using python3.6 instead of python3.7. Now, it's working.

Sorry and thank you for the tests @simonbray.

simonbray commented 2 years ago

Ah, that makes sense, BioBlend 0.1.17 requires Python >= 3.7, so Planemo does as well.

I updated the docs here: https://github.com/galaxyproject/planemo/commit/7f4c8f675f65b74ffe75c1e2d245ce88e38bf8bc. Thanks for reporting!