Comments (4)
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.
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.
Hi,
Two things of note:
- 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.
- 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.
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.
Related Issues (6)
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from decrippter.