problem after conda installation
matt-shenton opened this issue · comments
Hi there
I created an environment:
conda create -n nanoplot -c bioconda nanoplot
conda activate nanoplot
(nanoplot) $ NanoPlot -h Traceback (most recent call last): File "/lustre/home/mshenton/anaconda3/envs/nanoplot/bin/NanoPlot", line 6, in <module> from nanoplot.NanoPlot import main File "/lustre/home/mshenton/anaconda3/envs/nanoplot/lib/python3.5/site-packages/nanoplot/NanoPlot.py", line 20, in <module> import nanoplot.report as report File "/lustre/home/mshenton/anaconda3/envs/nanoplot/lib/python3.5/site-packages/nanoplot/report.py", line 106 html_info.append(f"{k}:\t{settings[k]}<br>") ^ SyntaxError: invalid syntax
Is this about my environment, or conda setup?
Here's what's in the environment. Thanks for any help
Cheers
Matt
`name: nanoplot
channels:
- defaults
- conda-forge
- bioconda
- r
dependencies: - _libgcc_mutex=0.1=main
- _openmp_mutex=4.5=1_gnu
- arrow-cpp=0.9.0=py35h165c0fa_7
- bcftools=1.8=h4da6232_3
- biopython=1.68=py35_0
- blas=1.0=mkl
- bzip2=1.0.8=h7b6447c_0
- ca-certificates=2022.3.18=h06a4308_0
- certifi=2020.6.20=pyhd3eb1b0_3
- curl=7.71.1=h8f29fe8_2
- deprecated=1.2.12=pyhd3eb1b0_0
- expat=2.4.4=h295c915_0
- font-ttf-dejavu-sans-mono=2.37=hd3eb1b0_0
- font-ttf-inconsolata=2.001=hcb22688_0
- font-ttf-source-code-pro=2.030=hd3eb1b0_0
- font-ttf-ubuntu=0.83=h8b1ccd4_0
- fontconfig=2.13.1=h6c09931_0
- fonts-conda-forge=1=0
- freetype=2.11.0=h70c0345_0
- htslib=1.7=0
- icu=58.2=he6710b0_3
- intel-openmp=2022.0.1=h06a4308_3633
- jpeg=9d=h7f8727e_0
- kaleido-core=0.2.1=h3644ca4_0
- krb5=1.19.2=hac12032_0
- libboost=1.65.1=habcd387_4
- libcurl=7.71.1=h303737a_2
- libdeflate=1.2=h516909a_1
- libedit=3.1.20210910=h7f8727e_0
- libevent=2.1.12=h8f2d780_0
- libffi=3.3=he6710b0_2
- libgcc=7.2.0=h69d50b8_2
- libgcc-ng=9.3.0=h5101ec6_17
- libgfortran-ng=7.5.0=ha8ba4b0_17
- libgfortran4=7.5.0=ha8ba4b0_17
- libgomp=9.3.0=h5101ec6_17
- libpng=1.6.37=hbc83047_0
- libprotobuf=3.5.2=h6f1eeef_0
- libssh2=1.9.0=h1ba5d50_1
- libstdcxx-ng=9.3.0=hd4cf53a_17
- libtiff=4.0.9=he85c1e1_2
- libuuid=1.0.3=h7f8727e_2
- libxml2=2.9.12=h03d6c58_0
- lz4-c=1.8.1.2=h14c3975_0
- mathjax=2.7.7=0
- mkl=2018.0.3=1
- mkl_fft=1.0.6=py35h7dd41cf_0
- mkl_random=1.0.1=py35h4414c95_1
- mmtf-python=1.0.2=py35_0
- msgpack-python=0.5.6=py35h6bb024c_1
- nanoget=1.16.1=py_0
- nanomath=1.2.1=pyhdfd78af_0
- nanoplot=1.36.1=pyhdfd78af_0
- ncurses=6.3=h7f8727e_2
- nspr=4.33=h295c915_0
- nss=3.74=h0370c37_0
- numpy=1.15.2=py35h1d66e8a_0
- numpy-base=1.15.2=py35h81de0dd_0
- olefile=0.46=py35_0
- openssl=1.1.1n=h7f8727e_0
- pandas=0.23.4=py35h04863e7_0
- parquet-cpp=1.4.0=h3238a2a_0
- pillow=5.2.0=py35heded4f4_0
- pip=10.0.1=py35_0
- plotly=4.14.3=pyhd3eb1b0_0
- pyarrow=0.9.0=py35hfc40096_2
- pysam=0.14.1=py35hae42fb6_1
- python=3.5.6=h12debd9_1
- python-dateutil=2.8.2=pyhd3eb1b0_0
- python-kaleido=0.2.1=pyhd8ed1ab_0
- pytz=2021.3=pyhd3eb1b0_0
- readline=8.1.2=h7f8727e_1
- reportlab=3.5.6=py35he686d34_0
- retrying=1.3.3=py35_2
- samtools=1.7=1
- scipy=1.1.0=py35hfa4b5c9_1
- setuptools=40.2.0=py35_0
- six=1.16.0=pyhd3eb1b0_1
- snappy=1.1.8=he6710b0_0
- sqlite=3.38.0=hc218d9a_0
- tbb=2021.5.0=hd09550d_0
- tbb4py=2018.0.5=py35h6bb024c_0
- thrift-cpp=0.11.0=h02b749d_3
- tk=8.6.11=h1ccaba5_0
- wheel=0.37.1=pyhd3eb1b0_0
- wrapt=1.10.11=py35h14c3975_2
- xz=5.2.5=h7b6447c_0
- zlib=1.2.11=h7f8727e_4
- zstd=1.3.3=h84994c4_0
prefix: /lustre/home/mshenton/anaconda3/envs/nanoplot
`
Hi,
NanoPlot requires minimally python 3.6, so that is most likely the cause of this error.
Best,
Wouter
Thanks for checking it out. I am not sure why my conda setup chose python 3.5 for this environment, the base one is 3.7. Anyway, I think this is a conda issue for me to investigate.
Thanks again for the tool and your help.
Best wishes
Matt