Error in setting up the environment

[jchariker]

Hi,

I used the following command:
conda create -n paqr_kapac -c bioconda -c ostrokach --file requirements_py3.txt

And I received this error message:
Collecting package metadata (current_repodata.json): done
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

• python==3.5.1
• docutils==0.12

Current channels:

• https://conda.anaconda.org/bioconda/linux-64
• https://conda.anaconda.org/bioconda/noarch
• https://conda.anaconda.org/ostrokach/linux-64
• https://conda.anaconda.org/ostrokach/noarch
• https://repo.anaconda.com/pkgs/main/linux-64
• https://repo.anaconda.com/pkgs/main/noarch
• https://repo.anaconda.com/pkgs/r/linux-64
• https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

Do you have any advice for solving this?
Thanks for your help!

[koljaLanger]

Hi
many thanks for your feedback!

May I ask you to try the following:
Instead of the initial command include conda-forge as channel and run the command as follows conda create -n paqr_kapac -c bioconda -c ostrokach -c conda-forge --file requirements_py3.txt

Please let us know if this solves the problem.

Best
Ralf

[jchariker]

Thank you for your quick response!

Using the following command:
conda create -n paqr_kapac -c bioconda -c ostrokach -c conda-forge --file requirements_py3.txt

I received the following information in the console:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Package xz conflicts for:
pyyaml==3.12 -> python[version='2.7.,3.4.,3.5.,>=3.5,<3.6.0a0,>=3.6,<3.7.0a0'] -> xz[version='5.2.,>=5.2.3,<5.3.0a0,>=5.2.3,<6.0a0,>=5.2.4,<5.3.0a0']
snakemake==3.13.0 -> pandas -> numpy[version='1.10.,1.12.,1.13.,>=1.11.3,<2.0a0,>=1.14.6,<2.0a0,>=1.9.'] -> mkl_random[version='>=1.0.2,<2.0a0'] -> numpy-base[version='>=1.0.2,<2.0a0'] -> python[version='>=3.5,<3.6.0a0,>=3.6,<3.7.0a0'] -> xz[version='5.2.,>=5.2.3,<5.3.0a0,>=5.2.3,<6.0a0,>=5.2.4,<5.3.0a0']
docutils==0.12 -> python[version='3.4.,>=3.5,<3.6.0a0'] -> xz[version='5.2.,>=5.2.3,<5.3.0a0,>=5.2.3,<6.0a0,>=5.2.4,<5.3.0a0']
r-optparse==1.3.2 -> r=3.3.1 -> r-recommended==3.3.1 -> r-survival -> r-matrix[version='>=1.2.12,<1.2.13.0a0'] -> r-lattice[version='>=0.20.35,<0.20.36.0a0'] -> r-base[version='3.1.3.,3.2.0.,3.2.1.,3.3.1.,3.3.2.,3.4.1.'] -> pango=1.40 -> harfbuzz[version='1.3.,>=1.7.4,<2.0a0,>=1.9.0,<2.0a0'] -> cairo[version='1.14.,>=1.14.12,<1.15.0a0,>=1.14.12,<2.0a0'] -> fontconfig[version='2.11.,2.12.,>=2.13.0,<3.0a0'] -> libxml2=2.9 -> xz[version='5.0.,5.2.,>=5.2.3,<6.0a0,>=5.2.4,<5.3.0a0,>=5.2.4,<6.0a0']
r-base==3.3.2 -> pango=1.40 -> harfbuzz[version='1.3.,>=1.7.4,<2.0a0,>=1.9.0,<2.0a0'] -> cairo[version='1.14.,>=1.14.12,<1.15.0a0,>=1.14.12,<2.0a0'] -> fontconfig[version='2.11.,2.12.,>=2.13.0,<3.0a0'] -> libxml2=2.9 -> xz[version='5.2.,>=5.2.3,<6.0a0,>=5.2.4,<5.3.0a0,>=5.2.4,<6.0a0']
numpy==1.11.3 -> numpy-base[version='>=1.0.2,<2.0a0'] -> python[version='>=2.7,<2.8.0a0,>=3.5,<3.6.0a0,>=3.6,<3.7.0a0,>=3.7,<3.8.0a0'] -> xz[version='5.2.,>=5.2.3,<5.3.0a0,>=5.2.3,<6.0a0,>=5.2.4,<5.3.0a0']
graphviz==2.38.0 -> pango[version='1.40.,>=1.40.14,<1.41.0a0'] -> harfbuzz[version='1.3.,>=1.7.4,<2.0a0,>=1.9.0,<2.0a0'] -> cairo[version='1.14.,>=1.14.12,<1.15.0a0,>=1.14.12,<2.0a0'] -> fontconfig[version='2.11.,2.12.,>=2.13.0,<3.0a0'] -> libxml2=2.9 -> xz[version='5.0.,5.2.,>=5.2.3,<6.0a0,>=5.2.4,<5.3.0a0,>=5.2.4,<6.0a0']
Package python conflicts for:
python==3.5.1
Package libxml2 conflicts for:
r-base==3.3.2 -> pango=1.40 -> harfbuzz[version='1.3.,>=1.7.4,<2.0a0,>=1.9.0,<2.0a0'] -> cairo[version='1.14.,>=1.14.12,<1.15.0a0,>=1.14.12,<2.0a0'] -> fontconfig[version='2.11.,2.12.,>=2.13.0,<3.0a0'] -> libxml2=2.9
graphviz==2.38.0 -> pango[version='1.40.,>=1.40.14,<1.41.0a0'] -> harfbuzz[version='1.3.,>=1.7.4,<2.0a0,>=1.9.0,<2.0a0'] -> cairo[version='1.14.,>=1.14.12,<1.15.0a0,>=1.14.12,<2.0a0'] -> fontconfig[version='2.11.,2.12.,>=2.13.0,<3.0a0'] -> libxml2=2.9
r-optparse==1.3.2 -> r=3.3.1 -> r-recommended==3.3.1 -> r-survival -> r-matrix[version='>=1.2.12,<1.2.13.0a0'] -> r-lattice[version='>=0.20.35,<0.20.36.0a0'] -> r-base[version='3.1.3.,3.2.0.,3.2.1.,3.3.1.,3.3.2.,3.4.1.'] -> pango=1.40 -> harfbuzz[version='1.3.,>=1.7.4,<2.0a0,>=1.9.0,<2.0a0'] -> cairo[version='1.14.,>=1.14.12,<1.15.0a0,>=1.14.12,<2.0a0'] -> fontconfig[version='2.11.,2.12.*,>=2.13.0,<3.0a0'] -> libxml2=2.9

Thanks again for helping with this!

[koljaLanger]

Many thanks for the report.
I checked our environment again and, apparently, some of the package versions we use for our environment are not available anymore.

To solve this problem, I will assemble a new environment and come back to you soon.

Ralf

[jchariker]

Thank you, Ralf. I appreciate you taking the time to do that!
Julia

[koljaLanger]

Hi Julia

As far as I can tell, one of the packages we use in our environment (r-optparse) has changed to an extent that makes it incompatible with the rest of our environment.
In order to circumvent this problem, I established another requirements file called requirements_py3_UPDATED.txt that should be used instead. Next, the missing package r-optparse must be installed manually. I included a short paragraph for this in the README file. Can you please check again and let us know if this solves your problem?

Best
Ralf

[jchariker]

Hi Ralf,
Your instructions were very clear, and I had no errors during installation. Thank you for quickly finding these solutions so that I can move forward with my analysis! I am now working on getting my input files together and editing the config.yaml file where needed.
Julia