Can't download latest tracy 0.5.7 via conda
bomsterr opened this issue · 16 comments
I tried download Tracy on my conda as documented here: https://anaconda.org/bioconda/tracy.
However, this installs the old version (version: 0.5.3) and not the most recent 0.5.7 version. Is this a glitch on conda? I was able to download recent version as a statically linked binary.
That can happen if you have installed multiple tools in your conda environment and these request different versions of the dependencies. I am not sure how conda resolves these conflicts and in what order but in any case you can request a specific version using
conda install -c bioconda tracy==0.5.7
I tried your code and got the following error:
I am in my base environment though so I am not sure why tracy is conflicting with these other packages.
As I suspected, incompatible packages. I would either use the static binary or install a second, new conda environment.
okay thank you. Do you know what python version is compatible with Tracy?
Tracy is written in C++, it does not require python. The bioconda recipe states the dependencies:
I was also unable to install 0.5.7 in a clean conda environment.
Make sure you are outside any previous installed conda environment when you install a new one.
conda deactivate
Then you can install a new one, let's say in ~/testconda/. I just tried this using Mac and Linux and it works fine.
Linux:
wget 'https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh' && bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/testconda && ~/testconda/bin/conda install -y tracy && ~/testconda/bin/tracy --version
Mac OSX:
wget 'https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh' && bash Miniconda3-latest-MacOSX-x86_64.sh -b -p ~/testconda && ~/testconda/bin/conda install -y tracy && ~/testconda/bin/tracy --version
Can you please try this?
I tried your last code and I got this:
`
sqlite pkgs/main/linux-64::sqlite-3.33.0-h62c20be_0
tk pkgs/main/linux-64::tk-8.6.10-hbc83047_0
tqdm pkgs/main/noarch::tqdm-4.51.0-pyhd3eb1b0_0
urllib3 pkgs/main/noarch::urllib3-1.25.11-py_0
wheel pkgs/main/noarch::wheel-0.35.1-pyhd3eb1b0_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3
Preparing transaction: done
Executing transaction: done
installation finished.
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- tracy
Current channels:
- 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.
`
You need to add the bioconda channel.
conda install -c bioconda tracy=0.5.8
this time I got:
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort. failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Package xz conflicts for:
tracy=0.5.8 -> htslib[version='>=1.12,<1.13.0a0'] -> xz[version='>=5.2.4,<5.3.0a0|>=5.2.5,<5.3.0a0']
python=3.8 -> xz[version='>=5.2.4,<6.0a0|>=5.2.5,<6.0a0']
Package libgcc-ng conflicts for:
tracy=0.5.8 -> libgcc-ng[version='>=7.5.0|>=9.3.0']
tracy=0.5.8 -> bzip2[version='>=1.0.8,<2.0a0'] -> libgcc-ng[version='>=7.2.0|>=7.3.0']
following your instructions:
First I did:
conda deactivate
Then:
wget 'https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh' && bash Miniconda3-latest-Linux- x86_64.sh -b -p ~/testconda
Then:
~/testconda/bin/conda install -c bioconda tracy=0.5.8
And I got the error above
Thanks for reporting. I lately also had problems because of conda channel priorities as in this issue. This should work as your last command:
~/testconda/bin/conda install --strict-channel-priority --override-channels -c conda-forge -c bioconda -c defaults tracy
Can you please try this?
Now it worked. Thank you very much.
I have another question, if I may. when I run tracy decompose with whole reference genome (hg19) it says:
Only single-chromosome FASTA files are supported.
And when I run it with single reference genome (e.g. chr1 only), it says:
Reference is larger than 50Kbp. Please use a smaller reference slice or an indexed genome!
what format of reference genome is needed?
Thanks
As written in the documentation, you need to download the reference genome indices here. This works for entire genomes. The FASTA option is only for small reference slices (<50kbp).
I have just noticed that. Thank you very much.
Thanks. Since the installation issue is fixed, I will close this issue. If you have further questions just open a new one.