Tools: nf-core list hiccup

Created on 9 Oct 2018  路  11Comments  路  Source: nf-core/tools

Hello,
Here are the commands I used and the errors I get:


Click to expand installation log

Orens-MacBook-Pro:nf-core-tools oren$ pip3 install nf-core
Collecting nf-core
  Downloading https://files.pythonhosted.org/packages/9a/10/d4419093c0cc66d856df1a45c3b5c4548600d403596afbf77224dff4b571/nf-core-1.2.tar.gz (53kB)
    100% |鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅| 61kB 456kB/s 
Collecting cookiecutter (from nf-core)
  Downloading https://files.pythonhosted.org/packages/16/99/1ca3a75978270288354f419e9166666801cf7e7d8df984de44a7d5d8b8d0/cookiecutter-1.6.0-py2.py3-none-any.whl (50kB)
    100% |鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅| 51kB 252kB/s 
Collecting click (from nf-core)
  Downloading https://files.pythonhosted.org/packages/fa/37/45185cb5abbc30d7257104c434fe0b07e5a195a6847506c074527aa599ec/Click-7.0-py2.py3-none-any.whl (81kB)
    100% |鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅| 81kB 317kB/s 
Collecting GitPython (from nf-core)
  Downloading https://files.pythonhosted.org/packages/fe/e5/fafe827507644c32d6dc553a1c435cdf882e0c28918a5bab29f7fbebfb70/GitPython-2.1.11-py2.py3-none-any.whl (448kB)
    100% |鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅| 450kB 625kB/s 
Collecting pyyaml (from nf-core)
  Downloading https://files.pythonhosted.org/packages/9e/a3/1d13970c3f36777c583f136c136f804d70f500168edc1edea6daa7200769/PyYAML-3.13.tar.gz (270kB)
    100% |鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅| 276kB 450kB/s 
Collecting requests (from nf-core)
  Downloading https://files.pythonhosted.org/packages/65/47/7e02164a2a3db50ed6d8a6ab1d6d60b69c4c3fdf57a284257925dfc12bda/requests-2.19.1-py2.py3-none-any.whl (91kB)
    100% |鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅| 92kB 394kB/s 
Collecting requests_cache (from nf-core)
  Downloading https://files.pythonhosted.org/packages/00/62/9e45a38988cb48c474805a1626439f4d9a486a042bd077af888fa8b17a64/requests_cache-0.4.13-py2.py3-none-any.whl
Collecting tabulate (from nf-core)
  Using cached https://files.pythonhosted.org/packages/12/c2/11d6845db5edf1295bc08b2f488cf5937806586afe42936c3f34c097ebdc/tabulate-0.8.2.tar.gz
Collecting poyo>=0.1.0 (from cookiecutter->nf-core)
  Downloading https://files.pythonhosted.org/packages/e0/16/e00e3001007a5e416ca6a51def6f9e4be6a774bf1c8486d20466f834d113/poyo-0.4.2-py2.py3-none-any.whl
Collecting future>=0.15.2 (from cookiecutter->nf-core)
  Downloading https://files.pythonhosted.org/packages/00/2b/8d082ddfed935f3608cc61140df6dcbf0edea1bc3ab52fb6c29ae3e81e85/future-0.16.0.tar.gz (824kB)
    100% |鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅| 829kB 383kB/s 
Collecting binaryornot>=0.2.0 (from cookiecutter->nf-core)
  Downloading https://files.pythonhosted.org/packages/24/7e/f7b6f453e6481d1e233540262ccbfcf89adcd43606f44a028d7f5fae5eb2/binaryornot-0.4.4-py2.py3-none-any.whl
Collecting jinja2-time>=0.1.0 (from cookiecutter->nf-core)
  Downloading https://files.pythonhosted.org/packages/6a/a1/d44fa38306ffa34a7e1af09632b158e13ec89670ce491f8a15af3ebcb4e4/jinja2_time-0.2.0-py2.py3-none-any.whl
Collecting jinja2>=2.7 (from cookiecutter->nf-core)
  Using cached https://files.pythonhosted.org/packages/7f/ff/ae64bacdfc95f27a016a7bed8e8686763ba4d277a78ca76f32659220a731/Jinja2-2.10-py2.py3-none-any.whl
Collecting whichcraft>=0.4.0 (from cookiecutter->nf-core)
  Downloading https://files.pythonhosted.org/packages/60/8a/5c52e30e11672f7e3aa61f348ddae443d122bcd96bc8b785ac76dbae944b/whichcraft-0.4.1-py2.py3-none-any.whl
Collecting gitdb2>=2.0.0 (from GitPython->nf-core)
  Downloading https://files.pythonhosted.org/packages/a9/fb/d3afc4e2a8d506a07af19f125f7a473ae1b56f942ed2ba80776eb8ae23b1/gitdb2-2.0.4-py2.py3-none-any.whl (62kB)
    100% |鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅| 71kB 244kB/s 
Collecting certifi>=2017.4.17 (from requests->nf-core)
  Downloading https://files.pythonhosted.org/packages/df/f7/04fee6ac349e915b82171f8e23cee63644d83663b34c539f7a09aed18f9e/certifi-2018.8.24-py2.py3-none-any.whl (147kB)
    100% |鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅| 153kB 342kB/s 
Collecting urllib3<1.24,>=1.21.1 (from requests->nf-core)
  Downloading https://files.pythonhosted.org/packages/bd/c9/6fdd990019071a4a32a5e7cb78a1d92c53851ef4f56f62a3486e6a7d8ffb/urllib3-1.23-py2.py3-none-any.whl (133kB)
    100% |鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅| 143kB 522kB/s 
Collecting chardet<3.1.0,>=3.0.2 (from requests->nf-core)
  Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl
Collecting idna<2.8,>=2.5 (from requests->nf-core)
  Downloading https://files.pythonhosted.org/packages/4b/2a/0276479a4b3caeb8a8c1af2f8e4355746a97fab05a372e4a2c6a6b876165/idna-2.7-py2.py3-none-any.whl (58kB)
    100% |鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅| 61kB 506kB/s 
Collecting arrow (from jinja2-time>=0.1.0->cookiecutter->nf-core)
  Downloading https://files.pythonhosted.org/packages/e0/86/4eb5228a43042e9a80fe8c84093a8a36f5db34a3767ebd5e1e7729864e7b/arrow-0.12.1.tar.gz (65kB)
    100% |鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅鈻堚枅| 71kB 796kB/s 
Collecting MarkupSafe>=0.23 (from jinja2>=2.7->cookiecutter->nf-core)
  Using cached https://files.pythonhosted.org/packages/4d/de/32d741db316d8fdb7680822dd37001ef7a448255de9699ab4bfcbdf4172b/MarkupSafe-1.0.tar.gz
Collecting smmap2>=2.0.0 (from gitdb2>=2.0.0->GitPython->nf-core)
  Downloading https://files.pythonhosted.org/packages/0f/14/e3112808b727f72df9531fc2f00b84d4966e66001748b6883a21c767e902/smmap2-2.0.4-py2.py3-none-any.whl
Collecting python-dateutil (from arrow->jinja2-time>=0.1.0->cookiecutter->nf-core)
  Using cached https://files.pythonhosted.org/packages/cf/f5/af2b09c957ace60dcfac112b669c45c8c97e32f94aa8b56da4c6d1682825/python_dateutil-2.7.3-py2.py3-none-any.whl
Collecting six>=1.5 (from python-dateutil->arrow->jinja2-time>=0.1.0->cookiecutter->nf-core)
  Using cached https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl
Building wheels for collected packages: nf-core, pyyaml, tabulate, future, arrow, MarkupSafe
  Running setup.py bdist_wheel for nf-core ... done
  Stored in directory: /Users/oren/Library/Caches/pip/wheels/07/58/3a/891755fa8288bb3e7d8013941ef13d1abf479513c7fdade5f3
  Running setup.py bdist_wheel for pyyaml ... done
  Stored in directory: /Users/oren/Library/Caches/pip/wheels/ad/da/0c/74eb680767247273e2cf2723482cb9c924fe70af57c334513f
  Running setup.py bdist_wheel for tabulate ... done
  Stored in directory: /Users/oren/Library/Caches/pip/wheels/2a/85/33/2f6da85d5f10614cbe5a625eab3b3aebfdf43e7b857f25f829
  Running setup.py bdist_wheel for future ... done
  Stored in directory: /Users/oren/Library/Caches/pip/wheels/bf/c9/a3/c538d90ef17cf7823fa51fc701a7a7a910a80f6a405bf15b1a
  Running setup.py bdist_wheel for arrow ... done
  Stored in directory: /Users/oren/Library/Caches/pip/wheels/a3/dd/b2/d3b8d22e8136164c2e2c36ed42392531957cdf9c717065b28b
  Running setup.py bdist_wheel for MarkupSafe ... done
  Stored in directory: /Users/oren/Library/Caches/pip/wheels/33/56/20/ebe49a5c612fffe1c5a632146b16596f9e64676768661e4e46
Successfully built nf-core pyyaml tabulate future arrow MarkupSafe
Installing collected packages: click, poyo, future, certifi, urllib3, chardet, idna, requests, binaryornot, six, python-dateutil, arrow, MarkupSafe, jinja2, jinja2-time, whichcraft, cookiecutter, smmap2, gitdb2, GitPython, pyyaml, requests-cache, tabulate, nf-core
Successfully installed GitPython-2.1.11 MarkupSafe-1.0 arrow-0.12.1 binaryornot-0.4.4 certifi-2018.8.24 chardet-3.0.4 click-7.0 cookiecutter-1.6.0 future-0.16.0 gitdb2-2.0.4 idna-2.7 jinja2-2.10 jinja2-time-0.2.0 nf-core-1.2 poyo-0.4.2 python-dateutil-2.7.3 pyyaml-3.13 requests-2.19.1 requests-cache-0.4.13 six-1.11.0 smmap2-2.0.4 tabulate-0.8.2 urllib3-1.23 whichcraft-0.4.1
Orens-MacBook-Pro:nf-core-tools oren$ pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git
-bash: pip: command not found
Orens-MacBook-Pro:nf-core-tools oren$ pip3 install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git
Collecting git+https://github.com/nf-core/tools.git
  Cloning https://github.com/nf-core/tools.git to /private/var/folders/rq/6p966k9971g8lfz6wx5w5z140000gn/T/pip-req-build-xy_c3ret
Collecting cookiecutter (from nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/16/99/1ca3a75978270288354f419e9166666801cf7e7d8df984de44a7d5d8b8d0/cookiecutter-1.6.0-py2.py3-none-any.whl
Collecting click (from nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/fa/37/45185cb5abbc30d7257104c434fe0b07e5a195a6847506c074527aa599ec/Click-7.0-py2.py3-none-any.whl
Collecting GitPython (from nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/fe/e5/fafe827507644c32d6dc553a1c435cdf882e0c28918a5bab29f7fbebfb70/GitPython-2.1.11-py2.py3-none-any.whl
Collecting pyyaml (from nf-core==1.2)
Collecting requests (from nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/65/47/7e02164a2a3db50ed6d8a6ab1d6d60b69c4c3fdf57a284257925dfc12bda/requests-2.19.1-py2.py3-none-any.whl
Collecting requests_cache (from nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/00/62/9e45a38988cb48c474805a1626439f4d9a486a042bd077af888fa8b17a64/requests_cache-0.4.13-py2.py3-none-any.whl
Collecting tabulate (from nf-core==1.2)
Collecting jinja2-time>=0.1.0 (from cookiecutter->nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/6a/a1/d44fa38306ffa34a7e1af09632b158e13ec89670ce491f8a15af3ebcb4e4/jinja2_time-0.2.0-py2.py3-none-any.whl
Collecting future>=0.15.2 (from cookiecutter->nf-core==1.2)
Collecting jinja2>=2.7 (from cookiecutter->nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/7f/ff/ae64bacdfc95f27a016a7bed8e8686763ba4d277a78ca76f32659220a731/Jinja2-2.10-py2.py3-none-any.whl
Collecting binaryornot>=0.2.0 (from cookiecutter->nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/24/7e/f7b6f453e6481d1e233540262ccbfcf89adcd43606f44a028d7f5fae5eb2/binaryornot-0.4.4-py2.py3-none-any.whl
Collecting whichcraft>=0.4.0 (from cookiecutter->nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/60/8a/5c52e30e11672f7e3aa61f348ddae443d122bcd96bc8b785ac76dbae944b/whichcraft-0.4.1-py2.py3-none-any.whl
Collecting poyo>=0.1.0 (from cookiecutter->nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/e0/16/e00e3001007a5e416ca6a51def6f9e4be6a774bf1c8486d20466f834d113/poyo-0.4.2-py2.py3-none-any.whl
Collecting gitdb2>=2.0.0 (from GitPython->nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/a9/fb/d3afc4e2a8d506a07af19f125f7a473ae1b56f942ed2ba80776eb8ae23b1/gitdb2-2.0.4-py2.py3-none-any.whl
Collecting chardet<3.1.0,>=3.0.2 (from requests->nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl
Collecting idna<2.8,>=2.5 (from requests->nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/4b/2a/0276479a4b3caeb8a8c1af2f8e4355746a97fab05a372e4a2c6a6b876165/idna-2.7-py2.py3-none-any.whl
Collecting urllib3<1.24,>=1.21.1 (from requests->nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/bd/c9/6fdd990019071a4a32a5e7cb78a1d92c53851ef4f56f62a3486e6a7d8ffb/urllib3-1.23-py2.py3-none-any.whl
Collecting certifi>=2017.4.17 (from requests->nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/df/f7/04fee6ac349e915b82171f8e23cee63644d83663b34c539f7a09aed18f9e/certifi-2018.8.24-py2.py3-none-any.whl
Collecting arrow (from jinja2-time>=0.1.0->cookiecutter->nf-core==1.2)
Collecting MarkupSafe>=0.23 (from jinja2>=2.7->cookiecutter->nf-core==1.2)
Collecting smmap2>=2.0.0 (from gitdb2>=2.0.0->GitPython->nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/0f/14/e3112808b727f72df9531fc2f00b84d4966e66001748b6883a21c767e902/smmap2-2.0.4-py2.py3-none-any.whl
Collecting python-dateutil (from arrow->jinja2-time>=0.1.0->cookiecutter->nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/cf/f5/af2b09c957ace60dcfac112b669c45c8c97e32f94aa8b56da4c6d1682825/python_dateutil-2.7.3-py2.py3-none-any.whl
Collecting six>=1.5 (from python-dateutil->arrow->jinja2-time>=0.1.0->cookiecutter->nf-core==1.2)
  Using cached https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl
Building wheels for collected packages: nf-core
  Running setup.py bdist_wheel for nf-core ... done
  Stored in directory: /private/var/folders/rq/6p966k9971g8lfz6wx5w5z140000gn/T/pip-ephem-wheel-cache-_0lo2wqa/wheels/7a/9d/0f/4fcfdede2e3c1932daacd92094f522c161c60d9060c6630f7c
Successfully built nf-core
Installing collected packages: MarkupSafe, jinja2, six, python-dateutil, arrow, jinja2-time, future, chardet, idna, urllib3, certifi, requests, binaryornot, whichcraft, poyo, click, cookiecutter, smmap2, gitdb2, GitPython, pyyaml, requests-cache, tabulate, nf-core
  Found existing installation: MarkupSafe 1.0
    Uninstalling MarkupSafe-1.0:
      Successfully uninstalled MarkupSafe-1.0
  Found existing installation: Jinja2 2.10
    Uninstalling Jinja2-2.10:
      Successfully uninstalled Jinja2-2.10
  Found existing installation: six 1.11.0
    Uninstalling six-1.11.0:
      Successfully uninstalled six-1.11.0
  Found existing installation: python-dateutil 2.7.3
    Uninstalling python-dateutil-2.7.3:
      Successfully uninstalled python-dateutil-2.7.3
  Found existing installation: arrow 0.12.1
    Uninstalling arrow-0.12.1:
      Successfully uninstalled arrow-0.12.1
  Found existing installation: jinja2-time 0.2.0
    Uninstalling jinja2-time-0.2.0:
      Successfully uninstalled jinja2-time-0.2.0
  Found existing installation: future 0.16.0
    Uninstalling future-0.16.0:
      Successfully uninstalled future-0.16.0
  Found existing installation: chardet 3.0.4
    Uninstalling chardet-3.0.4:
      Successfully uninstalled chardet-3.0.4
  Found existing installation: idna 2.7
    Uninstalling idna-2.7:
      Successfully uninstalled idna-2.7
  Found existing installation: urllib3 1.23
    Uninstalling urllib3-1.23:
      Successfully uninstalled urllib3-1.23
  Found existing installation: certifi 2018.8.24
    Uninstalling certifi-2018.8.24:
      Successfully uninstalled certifi-2018.8.24
  Found existing installation: requests 2.19.1
    Uninstalling requests-2.19.1:
      Successfully uninstalled requests-2.19.1
  Found existing installation: binaryornot 0.4.4
    Uninstalling binaryornot-0.4.4:
      Successfully uninstalled binaryornot-0.4.4
  Found existing installation: whichcraft 0.4.1
    Uninstalling whichcraft-0.4.1:
      Successfully uninstalled whichcraft-0.4.1
  Found existing installation: poyo 0.4.2
    Uninstalling poyo-0.4.2:
      Successfully uninstalled poyo-0.4.2
  Found existing installation: Click 7.0
    Uninstalling Click-7.0:
      Successfully uninstalled Click-7.0
  Found existing installation: cookiecutter 1.6.0
    Uninstalling cookiecutter-1.6.0:
      Successfully uninstalled cookiecutter-1.6.0
  Found existing installation: smmap2 2.0.4
    Uninstalling smmap2-2.0.4:
      Successfully uninstalled smmap2-2.0.4
  Found existing installation: gitdb2 2.0.4
    Uninstalling gitdb2-2.0.4:
      Successfully uninstalled gitdb2-2.0.4
  Found existing installation: GitPython 2.1.11
    Uninstalling GitPython-2.1.11:
      Successfully uninstalled GitPython-2.1.11
  Found existing installation: PyYAML 3.13
    Uninstalling PyYAML-3.13:
      Successfully uninstalled PyYAML-3.13
  Found existing installation: requests-cache 0.4.13
    Uninstalling requests-cache-0.4.13:
      Successfully uninstalled requests-cache-0.4.13
  Found existing installation: tabulate 0.8.2
    Uninstalling tabulate-0.8.2:
      Successfully uninstalled tabulate-0.8.2
  Found existing installation: nf-core 1.2
    Uninstalling nf-core-1.2:
      Successfully uninstalled nf-core-1.2
Successfully installed GitPython-2.1.11 MarkupSafe-1.0 arrow-0.12.1 binaryornot-0.4.4 certifi-2018.8.24 chardet-3.0.4 click-7.0 cookiecutter-1.6.0 future-0.16.0 gitdb2-2.0.4 idna-2.7 jinja2-2.10 jinja2-time-0.2.0 nf-core-1.2 poyo-0.4.2 python-dateutil-2.7.3 pyyaml-3.13 requests-2.19.1 requests-cache-0.4.13 six-1.11.0 smmap2-2.0.4 tabulate-0.8.2 urllib3-1.23 whichcraft-0.4.1

Rest of commands:

Orens-MacBook-Pro:nf-core-tools oren$ nf-core list

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

Traceback (most recent call last):
  File "/usr/local/bin/nf-core", line 198, in <module>
    nf_core_cli()
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/usr/local/bin/nf-core", line 70, in list
    nf_core.list.list_workflows(sort, json, keywords)
  File "/usr/local/lib/python3.7/site-packages/nf_core/list.py", line 35, in list_workflows
    wfs.get_local_nf_workflows()
  File "/usr/local/lib/python3.7/site-packages/nf_core/list.py", line 83, in get_local_nf_workflows
    nflist_raw = subprocess.check_output(['nextflow', 'list'], stderr=devnull)
  File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py", line 376, in check_output
    **kwargs).stdout
  File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py", line 453, in run
    with Popen(*popenargs, **kwargs) as process:
  File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py", line 756, in __init__
    restore_signals, start_new_session)
  File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py", line 1499, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'nextflow': 'nextflow'

Orens-MacBook-Pro:nf-core-tools oren$ pwd
/Users/oren/VIB/DATA_INTEGRATION/NextFlow/nf-core-tools

Orens-MacBook-Pro:nf-core-tools oren$ ls -ltr
total 72
-rw-r--r--   1 oren  staff   3286 Oct  9 19:40 CHANGELOG.md
-rw-r--r--   1 oren  staff    357 Oct  9 19:40 Dockerfile
-rw-r--r--   1 oren  staff   1064 Oct  9 19:40 LICENSE
-rw-r--r--   1 oren  staff     62 Oct  9 19:40 MANIFEST.in
-rw-r--r--   1 oren  staff  12381 Oct  9 19:40 README.md
drwxr-xr-x   4 oren  staff    128 Oct  9 19:40 bin
drwxr-xr-x   4 oren  staff    128 Oct  9 19:40 docs
drwxr-xr-x  11 oren  staff    352 Oct  9 19:40 nf_core
drwxr-xr-x   3 oren  staff     96 Oct  9 19:40 scripts
-rw-r--r--   1 oren  staff   1154 Oct  9 19:40 setup.py
drwxr-xr-x   7 oren  staff    224 Oct  9 19:40 tests



md5-b2fddd2ffe407347f9f9514783add498



Orens-MacBook-Pro:nf-core-tools oren$ ls nf_core/
__init__.py     create.py       licences.py     list.py         utils.py
bump_version.py     download.py     lint.py         pipeline-template



md5-b2fddd2ffe407347f9f9514783add498



Orens-MacBook-Pro:nf-core-tools oren$ nf-core list

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

Traceback (most recent call last):
  File "/usr/local/bin/nf-core", line 198, in <module>
    nf_core_cli()
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.7/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/usr/local/bin/nf-core", line 70, in list
    nf_core.list.list_workflows(sort, json, keywords)
  File "/usr/local/lib/python3.7/site-packages/nf_core/list.py", line 35, in list_workflows
    wfs.get_local_nf_workflows()
  File "/usr/local/lib/python3.7/site-packages/nf_core/list.py", line 83, in get_local_nf_workflows
    nflist_raw = subprocess.check_output(['nextflow', 'list'], stderr=devnull)
  File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py", line 376, in check_output
    **kwargs).stdout
  File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py", line 453, in run
    with Popen(*popenargs, **kwargs) as process:
  File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py", line 756, in __init__
    restore_signals, start_new_session)
  File "/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/subprocess.py", line 1499, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'nextflow': 'nextflow'
picture vibbits

All 11 comments

I updated your comment with some markdown tricks to try to make it a little more readable, hope that's ok @vibbits.

As @sven1103 asked on gitter:

@vibbits would you mind opening a python3.7 console and enter this:

import os
print(os.getenv('PATH'))

and afterwards from your terminal: which nextflow

However, irrespective of what is causing this, we should definitely handle the problem in a nicer manner with a better error message 馃憤

Phil

ewels picture ewels on 9 Oct 2018
👍1

Thanks guys. I tried as suggested and in python 3.7 did:

import os
print(os.getenv('PATH'))

And got: 

/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin

However, coming back to the terminal and asking 

which nextflow

yields empty output...

vibbits picture vibbits on 10 Oct 2018

Thanks @vibbits - so this looks like nextflow isn't installed.. But you said it was? How do you normally run nextflow if the command is not available on the PATH?

ewels picture ewels on 10 Oct 2018

Hmm..interesting!
I should say I never used nextflow before, but based on the installation commands log (see above), I thought I did managed to install nf with pip3. So I guess the installation did not succeed? Is there a way to debug my installation?

vibbits picture vibbits on 10 Oct 2018

You have to install Nextflow properly, like written on their website: https://www.nextflow.io/docs/latest/getstarted.html#installation.

Pip is a Python package manager, thus you cannot install Nextflow via pip.

After you installed Nextflow properly, the executable will be in your PATH variable scope, and nf-core will work properly.

Best, Sven

sven1103 picture sven1103 on 10 Oct 2018

Thank you @sven1103.
So o I try to install nextflow:

curl -s https://get.nextflow.io | bash

I get the following error:

Unable to find any JVMs matching version "1.8".
No Java runtime present, try --request to install.
/Users/oren/VIB/DATA_INTEGRATION/NextFlow/nextflow: line 313: /bin/java: No such file or directory
NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:
 JAVA_CMD: /bin/java
 NXF_OPTS:

But I do have java:

$ which java
/usr/bin/java

Any idea what im doing wrong?
Thanks and sorry for hustle :)

vibbits picture vibbits on 10 Oct 2018

If you're on OSX, install Java first: https://www.oracle.com/technetwork/java/javase/downloads/index.html

apeltzer picture apeltzer on 10 Oct 2018
👍1

I should say I never used nextflow before, but based on the installation commands log (see above), I thought I did managed to install nf with pip3. So I guess the installation did not succeed? Is there a way to debug my installation?

Ah, I think maybe you missed that nf-core and nextflow are separate tools perhaps? The Python nf-core tools package is a bunch of helper scripts to make it easier to use and develop nf-core pipelines. This is totally separate from nextflow itself, which is the package that actually does all the hard work :)

Our "getting started" documentation may be helpful: https://nf-co.re/usage_docs

ewels picture ewels on 10 Oct 2018
👍1

Indeed this threw me off. Now im on top of things. Thanks a lot!

vibbits picture vibbits on 10 Oct 2018

@vibbits does this mean that it works now?

sven1103 picture sven1103 on 10 Oct 2018

Yes. Please ignore my last comment @sven1103
it was solved by adding the full path of the folder before executing nextflow.
Cheers!

vibbits picture vibbits on 10 Oct 2018
🎉1
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