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Alexamk avatar Alexamk commented on July 29, 2024

Hi. Sorry to hear that. Are you sure it's numpy? It should be available for python2.

I've tried myself and run into the error that scikit-learn v. 0.11 is no longer available through Conda.
Unfortunately, that is the only real version requirement to the pipeline (the rest should work fine), which is also the reason it was written in python 2. The models were trained in that version, and can not be ported easily to another version.

My recommendation would be to try and install through pip, and leave out the version requirements except for scikit-learn==0.11. Or set up a conda environment, install all packages except scikit-learn, then install scikit-learn through pip afterwards.

from decrippter.

jowodo avatar jowodo commented on July 29, 2024

INPUT:

VERSION=0.0.0
URL=https://github.com/Alexamk/decRiPPter
DESCRIPTION="Genome mining tool for novel RiPP BGCs"
ENVNAME="decrippter"
LATESTVERSIONCMD='echo 0.0.0' # https://github.com/Alexamk/decRiPPter/issues/7
conda create -y -n $ENVNAME-$VERSION python=2.7
conda activate $ENVNAME-$VERSION
mkdir -p $CONDA_PREFIX/share
git clone -q $URL $CONDA_PREFIX/share/decrippter
conda install -c bioconda blast=2.6 diamond=0.9.31.132 hmmer=3.1b2 mcl muscle prodigal antismash

OUTPUT (from last command):

Channels:
 - bioconda
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: \ warning  libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides requested diamond 0.9.31.132**
  - nothing provides matplotlib-base 3.0.1 py37hc2fb212_1001 needed by matplotlib-3.0.1-h8a2030e_1001

Could not solve for environment specs
The following packages are incompatible
__ antismash is installable with the potential options
_  __ antismash [4.0.1|4.0.2|4.1.0] would require
_  _  __ matplotlib with the potential options
_  _  _  __ matplotlib [1.5.3|2.2.5] would require
_  _  _  _  __ pyqt with the potential options
_  _  _  _     __ pyqt [4.11.4|5.12.3|5.6.0|5.9.2] would require
_  _  _  _     _  __ qt [4.8.* |5.6.* |...|>=5.6.2,<5.7.0a0 ] with the potential options
_  _  _  _     _     __ qt [4.8.7|5.12.5|...|5.9.7] would require
_  _  _  _     _     _  __ gst-plugins-base >=1.12.5,<1.13.0a0 , which requires
_  _  _  _     _     _  _  __ xz >=5.2.4,<6.0.0a0 , which can be installed;
_  _  _  _     _     _  __ gstreamer [>=1.12.5,<1.13.0a0 |>=1.14.4,<1.15.0a0 ], which requires
_  _  _  _     _     _  _  __ xz >=5.2.4,<6.0.0a0 , which can be installed;
_  _  _  _     _     _  __ libtiff >=4.0.10,<4.5.0a0  with the potential options
_  _  _  _     _     _  _  __ libtiff [4.0.10|4.1.0] would require
_  _  _  _     _     _  _  _  __ xz >=5.2.4,<6.0.0a0 , which can be installed;
_  _  _  _     _     _  _  __ libtiff [4.1.0|4.2.0|4.3.0|4.4.0] would require
_  _  _  _     _     _  _  _  __ xz >=5.2.5,<6.0.0a0 , which can be installed;
_  _  _  _     _     _  _  __ libtiff 4.4.0 would require
_  _  _  _     _     _  _     __ xz [>=5.2.6,<6.0.0a0 |>=5.2.6,<6.0a0 ], which can be installed;
_  _  _  _     _     _  __ libxml2 [>=2.9.10,<3.0.0a0 |>=2.9.9,<3.0.0a0 ] with the potential options
_  _  _  _     _     _     __ libxml2 [2.10.0|2.10.1|...|2.9.14] would require
_  _  _  _     _     _     _  __ xz [>=5.2.6,<6.0.0a0 |>=5.2.6,<6.0a0 ], which can be installed;
_  _  _  _     _     _     __ libxml2 [2.9.10|2.9.11|2.9.12|2.9.13|2.9.14] would require
_  _  _  _     _     _     _  __ xz >=5.2.5,<6.0.0a0 , which can be installed;
_  _  _  _     _     _     __ libxml2 [2.9.10|2.9.9] would require
_  _  _  _     _     _        __ xz >=5.2.4,<6.0.0a0 , which can be installed;
_  _  _  _     _     __ qt 5.12.9 would require
_  _  _  _     _        __ libxml2 >=2.9.12,<3.0.0a0 , which can be installed (as previously explained);
_  _  _  _     __ pyqt [4.11.4|5.6.0] would require
_  _  _  _     _  __ python [3.5* |>=3.5,<3.6.0a0 ], which can be installed;
_  _  _  _     __ pyqt [4.11.4|5.6.0] would require
_  _  _  _     _  __ python 3.6* , which can be installed;
_  _  _  _     __ pyqt [5.12.3|5.6.0|5.9.2] would require
_  _  _  _     _  __ python >=3.6,<3.7.0a0 , which can be installed;
_  _  _  _     __ pyqt [5.12.3|5.15.4|5.15.7|5.6.0|5.9.2] would require
_  _  _  _     _  __ pyqtwebengine 5.12.1 py37he336c9b_5, which requires
_  _  _  _     _  _  __ python >=3.7,<3.8.0a0 , which can be installed;
_  _  _  _     _  __ python >=3.7,<3.8.0a0 , which can be installed;
_  _  _  _     __ pyqt 4.11.4 would require
_  _  _  _     _  __ python 3.4* , which can be installed;
_  _  _  _     __ pyqt [5.12.3|5.15.4|5.15.7|5.15.9] would require
_  _  _  _     _  __ python >=3.10,<3.11.0a0 , which can be installed;
_  _  _  _     __ pyqt [5.12.3|5.15.4|5.15.7|5.15.9] would require
_  _  _  _     _  __ python >=3.8,<3.9.0a0 , which can be installed;
_  _  _  _     __ pyqt [5.12.3|5.15.4|5.15.7|5.15.9] would require
_  _  _  _     _  __ python >=3.9,<3.10.0a0 , which can be installed;
_  _  _  _     __ pyqt [5.15.7|5.15.9] would require
_  _  _  _     _  __ python >=3.11,<3.12.0a0 , which can be installed;
_  _  _  _     __ pyqt 5.15.9 would require
_  _  _  _        __ python >=3.12.0rc3,<3.13.0a0  with the potential options
_  _  _  _           __ python [3.12.0|3.12.1], which can be installed;
_  _  _  _           __ python 3.12.0rc3 would require
_  _  _  _              __ _python_rc, which does not exist (perhaps a missing channel);
_  _  _  __ matplotlib 1.5.3 would require
_  _  _  _  __ pyqt 4.11.* , which can be installed (as previously explained);
_  _  _  __ matplotlib 1.5.3 would require
_  _  _  _  __ python 3.4* , which can be installed;
_  _  _  __ matplotlib 1.5.3 would require
_  _  _  _  __ python 3.5* , which can be installed;
_  _  _  __ matplotlib [2.1.2|2.2.4] would require
_  _  _  _  __ pyqt >=5.9.2,<5.10.0a0 , which can be installed (as previously explained);
_  _  _  __ matplotlib [2.1.2|2.2.3|...|3.3.4] would require
_  _  _  _  __ python >=3.6,<3.7.0a0 , which can be installed;
_  _  _  __ matplotlib [2.1.2|2.2.3|...|3.5.3] would require
_  _  _  _  __ python >=3.7,<3.8.0a0 , which can be installed;
_  _  _  __ matplotlib 2.2.3 would require
_  _  _  _  __ pyqt >=5.6.0,<5.7.0a0 , which can be installed (as previously explained);
_  _  _  __ matplotlib 2.2.4 would require
_  _  _  _  __ pyqt >=5.12.3,<5.13.0a0 , which can be installed (as previously explained);
_  _  _  __ matplotlib [2.2.4|3.1.1|...|3.7.3] would require
_  _  _  _  __ python >=3.8,<3.9.0a0 , which can be installed;
_  _  _  __ matplotlib 3.0.1 would require
_  _  _  _  __ matplotlib-base 3.0.1 py37hc2fb212_1001, which does not exist (perhaps a missing channel);
_  _  _  __ matplotlib 3.0.2 would require
_  _  _  _  __ matplotlib-base 3.0.2 py36h167e16e_1000, which does not exist (perhaps a missing channel);
_  _  _  __ matplotlib 3.0.2 would require
_  _  _  _  __ matplotlib-base 3.0.2 py36h167e16e_1001, which does not exist (perhaps a missing channel);
_  _  _  __ matplotlib 3.0.2 would require
_  _  _  _  __ matplotlib-base 3.0.2 py37h167e16e_1001, which does not exist (perhaps a missing channel);
_  _  _  __ matplotlib [3.2.0|3.2.1|3.2.2|3.3.0|3.3.1] would require
_  _  _  _  __ matplotlib-base [>=3.2.0,<3.2.1.0a0 |>=3.2.1,<3.2.2.0a0 |>=3.2.2,<3.2.3.0a0 |>=3.3.0,<3.3.1.0a0 |>=3.3.1,<3.3.2.0a0 ] with the potential options
_  _  _  _     __ matplotlib-base [3.2.0|3.2.1|...|3.3.2] would require
_  _  _  _     _  __ python >=3.6,<3.7.0a0 , which can be installed;
_  _  _  _     __ matplotlib-base [3.2.0|3.2.1|...|3.3.2] would require
_  _  _  _     _  __ python >=3.7,<3.8.0a0 , which can be installed;
_  _  _  _     __ matplotlib-base [3.2.0|3.2.1|...|3.3.2] would require
_  _  _  _        __ python >=3.8,<3.9.0a0 , which can be installed;
_  _  _  __ matplotlib 3.3.2 would require
_  _  _  _  __ matplotlib-base >=3.3.2,<3.3.3.0a0  with the potential options
_  _  _  _     __ matplotlib-base [3.2.0|3.2.1|...|3.3.2], which can be installed (as previously explained);
_  _  _  _     __ matplotlib-base [3.2.0|3.2.1|...|3.3.2], which can be installed (as previously explained);
_  _  _  _     __ matplotlib-base [3.2.0|3.2.1|...|3.3.2], which can be installed (as previously explained);
_  _  _  _     __ matplotlib-base 3.3.2 would require
_  _  _  _        __ python >=3.9,<3.10.0a0 , which can be installed;
_  _  _  __ matplotlib [3.3.2|3.3.3|...|3.8.3] would require
_  _  _  _  __ python >=3.9,<3.10.0a0 , which can be installed;
_  _  _  __ matplotlib [3.4.3|3.5.0|...|3.8.3] would require
_  _  _  _  __ python >=3.10,<3.11.0a0 , which can be installed;
_  _  _  __ matplotlib [3.6.1|3.6.2|...|3.8.3] would require
_  _  _  _  __ python >=3.11,<3.12.0a0 , which can be installed;
_  _  _  __ matplotlib [3.8.0|3.8.1|3.8.2|3.8.3] would require
_  _  _     __ python >=3.12,<3.13.0a0 , which can be installed;
_  _  __ xz 5.2.2 , which conflicts with any installable versions previously reported;
_  __ antismash 4.2.0 would require
_  _  __ blast 2.2.* , which can be installed;
_  __ antismash [5.1.1|5.1.2] would require
_  _  __ python >=3  with the potential options
_  _     __ python [3.10.0|3.10.1|...|3.10.9], which can be installed;
_  _     __ python [3.11.0|3.11.1|...|3.11.7], which can be installed;
_  _     __ python 3.4.5, which can be installed;
_  _     __ python [3.5.1|3.5.2|3.5.3|3.5.4|3.5.5], which can be installed;
_  _     __ python [3.6.0|3.6.1|...|3.6.9], which can be installed;
_  _     __ python [3.6.0a3|3.6.0a4|...|3.6.0rc1], which can be installed;
_  _     __ python [3.7.0|3.7.1|...|3.7.9], which can be installed;
_  _     __ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
_  _     __ python [3.9.0|3.9.1|...|3.9.9], which can be installed;
_  _     __ python [3.12.0|3.12.1], which can be installed;
_  _     __ python 3.12.0rc3, which cannot be installed (as previously explained);
_  __ antismash 5.1.2 would require
_  _  __ python >=3.5  with the potential options
_  _     __ python [3.10.0|3.10.1|...|3.10.9], which can be installed;
_  _     __ python [3.11.0|3.11.1|...|3.11.7], which can be installed;
_  _     __ python [3.5.1|3.5.2|3.5.3|3.5.4|3.5.5], which can be installed;
_  _     __ python [3.6.0|3.6.1|...|3.6.9], which can be installed;
_  _     __ python [3.6.0a3|3.6.0a4|...|3.6.0rc1], which can be installed;
_  _     __ python [3.7.0|3.7.1|...|3.7.9], which can be installed;
_  _     __ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
_  _     __ python [3.9.0|3.9.1|...|3.9.9], which can be installed;
_  _     __ python [3.12.0|3.12.1], which can be installed;
_  _     __ python 3.12.0rc3, which cannot be installed (as previously explained);
_  __ antismash [6.0.0|6.0.1|6.1.0|6.1.1] would require
_  _  __ python >=3.7  with the potential options
_  _     __ python [3.10.0|3.10.1|...|3.10.9], which can be installed;
_  _     __ python [3.11.0|3.11.1|...|3.11.7], which can be installed;
_  _     __ python [3.7.0|3.7.1|...|3.7.9], which can be installed;
_  _     __ python [3.8.0|3.8.1|...|3.8.8], which can be installed;
_  _     __ python [3.9.0|3.9.1|...|3.9.9], which can be installed;
_  _     __ python [3.12.0|3.12.1], which can be installed;
_  _     __ python 3.12.0rc3, which cannot be installed (as previously explained);
_  __ antismash 7.1.0 would require
_     __ python >=3.9  with the potential options
_        __ python [3.10.0|3.10.1|...|3.10.9], which can be installed;
_        __ python [3.11.0|3.11.1|...|3.11.7], which can be installed;
_        __ python [3.9.0|3.9.1|...|3.9.9], which can be installed;
_        __ python [3.12.0|3.12.1], which can be installed;
_        __ python 3.12.0rc3, which cannot be installed (as previously explained);
__ blast 2.6**  is not installable because it conflicts with any installable versions previously reported;
__ diamond 0.9.31.132**  does not exist (perhaps a typo or a missing channel);
__ pin-1 is not installable because it requires
   __ python 2.7.* , which conflicts with any installable versions previously reported.

Pins seem to be involved in the conflict. Currently pinned specs:
 - python 2.7.* (labeled as 'pin-1')

from decrippter.

Alexamk avatar Alexamk commented on July 29, 2024

Hi,
Two things of note:

  1. antiSMASH should be installed in it's own environment if you're interested in running it in parallel. However, it has not been tested since antiSMASH 5.0, and since the latest version is 7.0, the results might not be so relevant. I'd recommend running without it, or running the latest version of antiSMASH yourself and comparing the results.
  2. The version requirements seem the main culprit. I believe the external packages (particularly BLAST and Diamond) should work fine with later versions. Please try to install as: conda install -c bioconda blast diamond hmmer=3 mcl muscle prodigal and see if it works. It worked fine on my end.

from decrippter.

jowodo avatar jowodo commented on July 29, 2024

Hi,

**1. **

Or set up a conda environment, install all packages except scikit-learn, then install scikit-learn through pip afterwards.

It seems that pip for python2 in conda is broken ...

2.
conda install -c bioconda blast diamond hmmer=3 mcl muscle prodigal worked for me with

$ conda list | grep -E "blast|diamond|hmmer|mcl|muscle|prodigal"
blast                     2.15.0          pl5321h6f7f691_1    bioconda
diamond                   2.1.9                h43eeafb_0    bioconda
hmmer                     3.4                  hdbdd923_0    bioconda
mcl                       22.282          pl5321h031d066_1    bioconda
muscle                    5.1                  h4ac6f70_3    bioconda
prodigal                  2.6.3                h031d066_7    bioconda

from decrippter.

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