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Hello, trying to install vsearch/cluster but got `...
# modules
l
Hello, trying to install vsearch/cluster but got
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ERROR    Module 'vsearch/cluster' not found in available modules
how can I fix this? Can someone help me, please :)
m
how did you try to install it?
l
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nf-core modules install vsearch/cluster
m
can you try 
nf-core --verbose m install vsearch/cluster
?
l
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nf-core --verbose m install vsearch/cluster


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\ 
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.5.2 - <https://nf-co.re>


DEBUG    sys.platform='linux', git_executable='git'                                                                                                  util.py:494
Pulling from 'nf-core/modules' (<https://github.com/nf-core/modules.git>) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Waiting for responseDEBUG    Popen(['git', 'version'], cwd=/tmp/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)                       cmd.py:1270
DEBUG    Popen(['git', 'fetch', '-v', '--progress', '--', 'origin'], cwd=/tmp/.config/nfcore/nf-core/modules, stdin=None, shell=False,               cmd.py:1270
         universal_newlines=True)                                                                                                                               
DEBUG    Popen(['git', 'checkout', 'master'], cwd=/tmp/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)            cmd.py:1270
DEBUG    Popen(['git', 'merge', 'origin/master'], cwd=/tmp/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)        cmd.py:1270
DEBUG    Got '/tmp/.config/nfcore/nf-core/modules' as path                                                                                          utils.py:369
DEBUG    Found a config cache, loading: /tmp/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json                                       utils.py:403
DEBUG    Using config file: /tmp/.config/nfcore/nf-core/modules/.nf-core.yml                                                                       utils.py:1501
DEBUG    Got '.' as path                                                                                                                            utils.py:369
DEBUG    Found a config cache, loading: /tmp/.nextflow/nf-core/wf-config-cache-636044805f5ccb3572fc02196.json                                       utils.py:403
DEBUG    Using config file: .nf-core.yml                                                                                                           utils.py:1501
DEBUG    sys.platform='linux', git_executable='git'                                                                                                  util.py:494
DEBUG    Popen(['git', 'checkout', 'master'], cwd=/tmp/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)            cmd.py:1270
DEBUG    Popen(['git', 'merge', 'origin/master'], cwd=/tmp/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)        cmd.py:1270
DEBUG    Got '/tmp/.config/nfcore/nf-core/modules' as path                                                                                          utils.py:369
DEBUG    Found a config cache, loading: /tmp/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json                                       utils.py:403
DEBUG    Using config file: /tmp/.config/nfcore/nf-core/modules/.nf-core.yml                                                                       utils.py:1501
WARNING  There was an error running the prettier pre-commit hook.                                                                              lint_utils.py:172
         STDOUT: [INFO] Installing environment for <https://github.com/pre-commit/mirrors-prettier>.                                                              
         [INFO] Once installed this environment will be reused.                                                                                                 
         [INFO] This may take a few minutes...                                                                                                                  
         An unexpected error has occurred: AssertionError:                                                                                                      
         Check the log at /tmp/.cache/pre-commit/pre-commit.log                                                                                                 
                                                                                                                                                                
         STDERR:                                                                                                                                                
DEBUG    Popen(['git', 'checkout', 'master'], cwd=/tmp/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)            cmd.py:1270
ERROR    Module 'vsearch/cluster' not found in available modules                                                                                  install.py:236
DEBUG    entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                              code.py:11
DEBUG    entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                            fence.py:10
DEBUG    entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                  blockquote.py:13
DEBUG    entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                                  hr.py:15
DEBUG    entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                             list.py:102
DEBUG    entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                    reference.py:10
DEBUG    entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                  html_block.py:35
DEBUG    entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                        heading.py:14
DEBUG    entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                      lheading.py:10
DEBUG    entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False                                                                    paragraph.py:11
╭─ info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                              │
│ Use the command nf-core modules list to view available modules.                                                                                              │
│                                                                                                                                                              │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
ERROR                                                                                                                                             __main__.py:91
m
can you remove the modules cache (`rm -rf ~/.config/nfcore/nf-core/modules) and try it again
l
same
m
and you still get the weird prettier error in the verbose log? can you post the log here?
l
yep but other modules are fine
also with the weird prettier error
m
can you show the contents of 
/tmp/.cache/pre-commit/pre-commit.log
i am curious if it is indeed just a red herring
l
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### version information
pre-commit version: 4.5.1 git --version: git version 2.52.0 sys.version: 3.14.2 | packaged by conda-forge | (main, Jan 26 2026, 195600) [GCC 14.3.0] sys.executable: /usr/local/bin/python3.14 os.name: posix sys.platform: linux
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### error information
An unexpected error has occurred: AssertionError:
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```
Traceback (most recent call last):
  File "/usr/local/lib/python3.14/site-packages/pre_commit/error_handler.py", line 73, in error_handler
    yield
  File "/usr/local/lib/python3.14/site-packages/pre_commit/main.py", line 429, in main
    return run(args.config, store, args)
  File "/usr/local/lib/python3.14/site-packages/pre_commit/commands/run.py", line 443, in run
    install_hook_envs(to_install, store)
    ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.14/site-packages/pre_commit/repository.py", line 229, in install_hook_envs
    _hook_install(hook)
    ~~~~~~~~~~~~~^^^^^^
  File "/usr/local/lib/python3.14/site-packages/pre_commit/repository.py", line 85, in _hook_install
    lang.install_environment(
    ~~~~~~~~~~~~~~~~~~~~~~~~^
        hook.prefix, hook.language_version, hook.additional_dependencies,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/usr/local/lib/python3.14/site-packages/pre_commit/languages/node.py", line 80, in install_environment
    assert prefix.exists('package.json')
           ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^
AssertionError
```
m
okay, might be unrelated.
the weird thing is that i can install that module.
what do you get if you do 
nf-core modules list remote
and search for it?
l
Not there
Which version do you have?
I already did and was not in the list
m
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"vsearch/cluster": {
                        "branch": "master",
                        "git_sha": "694b2cdc2d695926dc10ac149e59b7b5b563cef9",
with nf-core/tools 3.5.2
if you go to .config/nfcore/nf-core/modules, can you find it there?
l
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ls $HOME/.config/nf-core/cache_3.6.9/
 github_info.sqlite
m
that is the wrong cache i think
i meant 
/tmp/.config/nfcore/nf-core/modules/
l
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ls /tmp/.config/nfcore/nf-core/modules/modules/nf-core/vsearch/
 cluster   dereplicate   fastqfilter   sintax   sort   usearchglobal
they are there!
m
that's weird...
how does your 
modules.json
look like?
l
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{
  "name": "",
  "homePage": "",
  "repos": {
    "<https://github.com/nf-core/modules.git>": {
      "modules": {
        "nf-core": {
          "cat/fastq": {
            "branch": "master",
            "git_sha": "5d28ea7cfaebcfae6f74d1067ea766d8ff19dff3",
            "installed_by": [
              "modules"
            ]
          },
          "cutadapt": {
            "branch": "master",
            "git_sha": "624977dfaf562211e68a8a868ca80acc8461f1ac",
            "installed_by": [
              "modules"
            ]
          },
          "fastqc": {
            "branch": "master",
            "git_sha": "79b36b51048048374b642289bfe9e591ef56fe05",
            "installed_by": [
              "modules"
            ]
          },
          "minimap2/align": {
            "branch": "master",
            "git_sha": "5c9f8d5b7671237c906abadc9ff732b301ca15ca",
            "installed_by": [
              "modules"
            ]
          },
          "minimap2/index": {
            "branch": "master",
            "git_sha": "14980f759266eec42dac401fcafeb83d6c957b41",
            "installed_by": [
              "modules"
            ]
          },
          "multiqc": {
            "branch": "master",
            "git_sha": "575e1a4b51a9bad7a8cd1316a88fb85684ef7c7b",
            "installed_by": [
              "modules"
            ]
          },
          "nanoq": {
            "branch": "master",
            "git_sha": "4dd9d8439a429c7ee566e0e2347f76ddeef27e66",
            "installed_by": [
              "modules"
            ]
          },
          "samtools/cat": {
            "branch": "master",
            "git_sha": "f9edc59be2fe25bb6fc73ca4dfc0d28246f2a2d6",
            "installed_by": [
              "modules"
            ]
          },
          "samtools/faidx": {
            "branch": "master",
            "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a",
            "installed_by": [
              "modules"
            ]
          },
          "samtools/fastq": {
            "branch": "master",
            "git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9",
            "installed_by": [
              "modules"
            ]
          },
          "samtools/sort": {
            "branch": "master",
            "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7",
            "installed_by": [
              "modules"
            ]
          },
          "seqkit/seq": {
            "branch": "master",
            "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
            "installed_by": [
              "modules"
            ]
          }
        }
      },
      "subworkflows": {
        "nf-core": {
          "utils_nfcore_pipeline": {
            "branch": "master",
            "git_sha": "65f5e638d901a51534c68fd5c1c19e8112fb4df1",
            "installed_by": [
              "subworkflows"
            ]
          }
        }
      }
    }
  }
}
m
looks good...
can you try to install it in another pipeline?
l
Ok
same
I'm not sure is the only module missing
m
just out of curiosity: can you try with the dev version of tools 
pip install --upgrade --force-reinstall git+<https://github.com/nf-core/tools.git@dev>
l
I have pipx
m
pipx install git+<https://github.com/nf-core/tools.git@dev>
then 🙂
l
mmm
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pipx install --force git+<https://github.com/nf-core/tools.git@dev>
ERROR: Package 'nf-core' requires a different Python: 3.9.25 not in '<4,>=3.10'
Cannot determine package name from spec 'git+<https://github.com/nf-core/tools.git@dev>'. Check package spec for errors.

lcozzuto in 🌐 biocore in RNAseq3 on  v3.0 [!?] on ☁️  (eu-central-1) took 5s 
❯ python --version
Python 3.9.25
m
yes, python 3.9 is EOL-ed. so we bumped it to 3.10 (but i thought 3.5.2 already did that)
l
maybe I have some problem with that
let me fix that
so no again
now I have the right python (we have modules)
I reinstalled
and still not there
m
can you get it to autofill if you just do 
nf-core m install
?
l
ouch
I had an alias
using a singularity image
removing it and having a locally installed one worked
so I imagine using nf-core in a container is not the best option
thanks a lot for your help
m
Haha, interesting setup
l
Ehehe directly from biocontainers
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