Miniconda not creating environment from python2_environment.yml
bio-developer opened this issue · 3 comments
I tried to install viper_python2 using the given commands.
Normal viper environment was installed correctly using both miniconda3 or Anaconda3 but python2 based viper environment did not succeed.
$ conda env create -f python2_environment.yml -n viper_py2
Warning: you have pip-installed dependencies in your environment file, but you do not list pip itself as one of your conda dependencies. Conda may not use the correct pip to install your packages, and they may end up in the wrong place. Please add an explicit pip dependency. I'm adding one for you, but still nagging you.
Collecting package metadata (repodata.json): done
Solving environment: failed
ResolvePackageNotFound:
- freetype=2.5.5
- pillow==4.0.0=py27_0
- numpy==1.11.2=py27_0
- curl=7.45.0
- system=5.8
- libgcc=5.2.0
- sqlite=3.13.0
- openssl=1.0.2j
- zlib=1.2.8
- setuptools==27.2.0=py27_0
- readline=6.2
- libtiff=4.0.6
- tk=8.5.18
- mkl=11.3.3
- reportlab==3.3.0=py27_0
- jpeg==9b=0
- xz=5.2.2
- bcftools==1.3.1=1 -> zlib==1.2.8
- cython==0.25.2=py27_0
Further when I ran the Snakemake workflow.
snakemake --snakefile viper/viper.snakefile --cores=21
This happened
Job 13: Generating expression matrix using cufflinks counts
/bin/bash: /home/bioinfo1/anaconda3/envs/viper_py2/bin/python2.7: No such file or directory
Kindly help.
Hi, I have exactly the same problem wit python2_environment.yml. Any ideas on how to solve it?
My dirty solution was to copy the miniconda directory of python2.7 viper env to respective position in default (in my case anaconda3 location for envs), and it worked. But I do not recommend this due to instability issues that may arise.
I expect authentic solution from Viper developers.
Hi,
Thanks for taking the time to share potential solutions.
I have found the following two alternatives to VIPER and they install and run without issues:
ELVERS: https://github.com/dib-lab/elvers
ARMOR: https://github.com/csoneson/ARMOR