Closed peterk87 closed 6 months ago
splaisan
commented
9 months ago I just tried installing with conda from the MD info and it could not get some dependencies right. tensorflow 2.2.0, pin-1-1, bcftools 1.10 I stopped trying at that point, a more detailed yaml dependency list would help I believe. thanks for your support
philcharron-cfia
commented
9 months ago Thank you for giving our tool a try and for bringing this issue to our attention. We appreciate your patience and are here to support you through the installation process. To address the dependencies issue you encountered with conda, we recommend trying an alternative package manager, Mamba, which is designed to handle dependencies more efficiently. Here's how you can set it up:
conda create -n vd -y
conda activate vd
mamba install -c bioconda -c conda-forge -c charronp variantdetectiveIf you still face installation issues, it might be helpful to attempt the installation from source if you haven't yet. You can find detailed instructions for this method at the following link: https://github.com/OLF-Bioinformatics/VariantDetective#installation-from-source
Please give these steps a try and let us know if you encounter any further difficulties. We're committed to ensuring that you can successfully use VariantDetective.
splaisan
commented
9 months ago Thanks Phil,
I tried it once more although conda currently uses mamba by default. I first had to install mamba inside the created env as I do not have it in my base (installs a LOT of extra packages with itself).
It failed now on openssl (see below) Could python 3.6 be required for your package to work?
I will not attempt installing from source as my server does not allow it and wait until the conda install process gets revised and works to try again. Or else, if you create a working docker, I will be happy to give it a try.
Best regards,
Stephane
(base) u0002316@gbw-s-pacbio01:~ $ conda create -n variant_detective -y
Channels:
- defaults
- conda-forge
- bioconda
- r
- anaconda
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /opt/miniconda3/envs/variant_detective
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate variant_detective
#
# To deactivate an active environment, use
#
# $ conda deactivate
(base) u0002316@gbw-s-pacbio01:~ $ conda activate variant_detective
(variant_detective) u0002316@gbw-s-pacbio01:~ $ mamba install -c bioconda -c conda-forge -c charronp variantdetective
Command 'mamba' not found, did you mean:
command 'samba' from deb samba (2:4.15.13+dfsg-0ubuntu1.5)
Try: sudo apt install <deb name>
(variant_detective) u0002316@gbw-s-pacbio01:~ $ conda install mamba
Channels:
- defaults
- conda-forge
- bioconda
- r
- anaconda
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /opt/miniconda3/envs/variant_detective
added / updated specs:
- mamba
The following packages will be downloaded:
package | build
---------------------------|-----------------
bzip2-1.0.8 | h5eee18b_5 262 KB
requests-2.31.0 | py39h06a4308_1 96 KB
tzdata-2024a | h04d1e81_0 116 KB
urllib3-2.1.0 | py39h06a4308_1 156 KB
------------------------------------------------------------
Total: 630 KB
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
_openmp_mutex pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu
brotli-python pkgs/main/linux-64::brotli-python-1.0.9-py39h6a678d5_7
bzip2 pkgs/main/linux-64::bzip2-1.0.8-h5eee18b_5
c-ares pkgs/main/linux-64::c-ares-1.19.1-h5eee18b_0
ca-certificates pkgs/main/linux-64::ca-certificates-2023.12.12-h06a4308_0
certifi pkgs/main/linux-64::certifi-2024.2.2-py39h06a4308_0
cffi pkgs/main/linux-64::cffi-1.16.0-py39h5eee18b_0
charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0
conda pkgs/main/linux-64::conda-4.12.0-py39h06a4308_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-2.2.0-py39h06a4308_0
conda-package-str~ pkgs/main/linux-64::conda-package-streaming-0.9.0-py39h06a4308_0
cryptography pkgs/main/linux-64::cryptography-41.0.3-py39h130f0dd_0
icu pkgs/main/linux-64::icu-58.2-he6710b0_3
idna pkgs/main/linux-64::idna-3.4-py39h06a4308_0
krb5 pkgs/main/linux-64::krb5-1.20.1-h568e23c_1
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1
libarchive pkgs/main/linux-64::libarchive-3.5.2-h5de8990_0
libcurl pkgs/main/linux-64::libcurl-8.2.1-h91b91d3_0
libedit pkgs/main/linux-64::libedit-3.1.20230828-h5eee18b_0
libev pkgs/main/linux-64::libev-4.33-h7f8727e_1
libffi pkgs/main/linux-64::libffi-3.4.4-h6a678d5_0
libgcc-ng pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1
libgomp pkgs/main/linux-64::libgomp-11.2.0-h1234567_1
libiconv pkgs/main/linux-64::libiconv-1.16-h7f8727e_2
libnghttp2 pkgs/main/linux-64::libnghttp2-1.52.0-ha637b67_1
libsolv pkgs/main/linux-64::libsolv-0.7.24-he621ea3_0
libssh2 pkgs/main/linux-64::libssh2-1.10.0-h37d81fd_2
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1
libxml2 pkgs/main/linux-64::libxml2-2.9.14-h74e7548_0
lz4-c pkgs/main/linux-64::lz4-c-1.9.4-h6a678d5_0
mamba conda-forge/linux-64::mamba-0.17.0-py39h951de11_0
ncurses pkgs/main/linux-64::ncurses-6.4-h6a678d5_0
openssl pkgs/main/linux-64::openssl-1.1.1w-h7f8727e_0
pcre2 pkgs/main/linux-64::pcre2-10.42-hebb0a14_0
pip pkgs/main/linux-64::pip-23.3.1-py39h06a4308_0
pycosat pkgs/main/linux-64::pycosat-0.6.6-py39h5eee18b_0
pycparser pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
pyopenssl pkgs/main/linux-64::pyopenssl-23.2.0-py39h06a4308_0
pysocks pkgs/main/linux-64::pysocks-1.7.1-py39h06a4308_0
python pkgs/main/linux-64::python-3.9.18-h7a1cb2a_0
python_abi conda-forge/linux-64::python_abi-3.9-2_cp39
readline pkgs/main/linux-64::readline-8.2-h5eee18b_0
reproc pkgs/main/linux-64::reproc-14.2.4-h295c915_1
reproc-cpp pkgs/main/linux-64::reproc-cpp-14.2.4-h295c915_1
requests pkgs/main/linux-64::requests-2.31.0-py39h06a4308_1
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.100-py39h27cfd23_0
setuptools pkgs/main/linux-64::setuptools-68.2.2-py39h06a4308_0
sqlite pkgs/main/linux-64::sqlite-3.41.2-h5eee18b_0
tk pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0
tzdata pkgs/main/noarch::tzdata-2024a-h04d1e81_0
urllib3 pkgs/main/linux-64::urllib3-2.1.0-py39h06a4308_1
wheel pkgs/main/linux-64::wheel-0.41.2-py39h06a4308_0
xz pkgs/main/linux-64::xz-5.4.6-h5eee18b_0
yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
zlib pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0
zstandard pkgs/main/linux-64::zstandard-0.19.0-py39h5eee18b_0
zstd pkgs/main/linux-64::zstd-1.5.5-hc292b87_0
Proceed ([y]/n)?
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(variant_detective) u0002316@gbw-s-pacbio01:~ $ mamba install -c bioconda -c conda-forge -c charronp variantdetective
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
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/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
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████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
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██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.17.0) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['variantdetective']
charronp/linux-64 [====================] (00m:00s) Done
r/linux-64 [====================] (00m:00s) Done
anaconda/noarch [====================] (00m:00s) Done
pkgs/main/noarch [====================] (00m:00s) Done
bioconda/noarch [====================] (00m:01s) Done
bioconda/linux-64 [====================] (00m:01s) Done
r/noarch [====================] (00m:00s) Done
charronp/noarch [====================] (00m:00s) Done
anaconda/linux-64 [====================] (00m:00s) Done
pkgs/r/noarch [====================] (00m:00s) Done
conda-forge/noarch [====================] (00m:03s) Done
pkgs/r/linux-64 [====================] (00m:00s) Done
pkgs/main/linux-64 [====================] (00m:01s) Done
conda-forge/linux-64 [====================] (00m:07s) Done
Pinned packages:
- python 3.9.*
Encountered problems while solving:
- nothing provides openssl >=1.1.1,<1.1.2.0a0 needed by python-3.6.7-h0371630_0Thanks for trying my suggestions. Here are a couple comments:
I first had to install mamba inside the created env as I do not have it in my base (installs a LOT of extra packages with itself).
From the Mamba documentation, installing Mamba into any other environment than base is not supported. As you mentioned, mamba ends up installing many libraries and these would cause conflicts with the VariantDetective dependencies if installed in the same environment, If we ignore Mamba's recommendations about installing outside of base and you want to use a dedicated mamba environment, I was able to install VariantDetective using the following steps:
# Create a mamba environment
conda create -n mamba mamba
conda activate mamba
# From inside this environment, create a VariantDetective environment
mamba create -n variantdetective -c bioconda -c conda-forge -c charronp variantdetective
conda activate variantdetective Please try that out and let me know if that solves the issues.
Could python 3.6 be required for your package to work?
Yes, due to some tools needing that specific version of Python, the pipeline requires v3.6 currently.
I will not attempt installing from source as my server does not allow it and wait until the conda install process gets revised and works to try again.
If the server allows installing Python modules via pip, then the source installation is exactly that. However, you would know the restrictions of the server and I recommend following any steps that are allowed by your group.
Or else, if you create a working docker, I will be happy to give it a try.
That is something we can look into for the future, thanks for the recommendation.
It would be great to have VD in Bioconda for greater visibility and auto-building of new Conda packages for new releases of VD. Docker and Singularity containers are also created for all Bioconda packages, which is handy for developing containerized workflows.
https://bioconda.github.io/contributor/index.html
It's fairly simple to get a tool into Bioconda: make a PR to bioconda-recipes with a
meta.yamlof packages necessary for building/running VD.There's lots of examples to go based off of, e.g.