Can't download latest tracy 0.5.7 via conda

[bomsterr]

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.

[tobiasrausch]

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

[bomsterr]

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.

[tobiasrausch]

As I suspected, incompatible packages. I would either use the static binary or install a second, new conda environment.

[bomsterr]

okay thank you. Do you know what python version is compatible with Tracy?

[tobiasrausch]

Tracy is written in C++, it does not require python. The bioconda recipe states the dependencies:

Tracy bioconda recipe

[jomelby]

I was also unable to install 0.5.7 in a clean conda environment.

[tobiasrausch]

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?

[muntajihad]

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.
`

[tobiasrausch]

You need to add the bioconda channel.

conda install -c bioconda tracy=0.5.8

[muntajihad]

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']

[muntajihad]

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

[tobiasrausch]

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?

[muntajihad]

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

[tobiasrausch]

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).

[muntajihad]

I have just noticed that. Thank you very much.

[tobiasrausch]

Thanks. Since the installation issue is fixed, I will close this issue. If you have further questions just open a new one.