[bug] bactopia tools depend on uninstallable bioperl-1.7.2 #502
Comments
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Hmmm, this is an interesting one. This works for me Interestingly, I got Do you have anything in the condarc file other than the channels? Or does this by chance work for you? |
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So:
LibMambaUnsatisfiableError: Encountered problems while solving:
- package perl-bioperl-1.7.2-pl526_11 requires perl-bio-coordinate, but none of the providers can be installed
Could not solve for environment specs
The following packages are incompatible
├─ perl-bioperl ==1.7.2 pl526_11 is installable and it requires
│ └─ perl-bio-coordinate with the potential options
│ ├─ perl-bio-coordinate 1.007001 would require
│ │ └─ perl-parent with the potential options
│ │ ├─ perl-parent [0.236|0.238|0.239|0.240|0.241] would require
│ │ │ └─ perl >=5.32.1,<6.0a0 *_perl5, which can be installed;
│ │ └─ perl-parent 0.236 conflicts with any installable versions previously reported;
│ └─ perl-bio-coordinate 1.007001 would require
│ └─ perl >=5.32.1,<6.0a0 *_perl5, which can be installed;
└─ prokka ==1.14.6 pl5262hdfd78af_3 is not installable because it requires
├─ perl 5.26.2.* , which conflicts with any installable versions previously reported;
└─ perl-xml-simple with the potential options
├─ perl-xml-simple 2.22 would require
│ └─ perl >=5.22.0,<5.23.0 , which can be installed;
├─ perl-xml-simple [2.22|2.25] would require
│ └─ perl-xml-sax-expat with the potential options
│ ├─ perl-xml-sax-expat 0.51 would require
│ │ └─ perl >=5.32.1,<6.0a0 *_perl5, which can be installed;
│ └─ perl-xml-sax-expat 0.51 conflicts with any installable versions previously reported;
└─ perl-xml-simple 2.25 would require
└─ perl >=5.32.1,<6.0a0 *_perl5, which can be installed. |
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Hmmm, still can replicate here. Here's my base environment |
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My base environment: name: base
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- archspec=0.2.3=pyhd8ed1ab_0
- boltons=23.1.1=pyhd8ed1ab_0
- brotli-python=1.1.0=py310hc6cd4ac_1
- bzip2=1.0.8=hd590300_5
- c-ares=1.24.0=hd590300_0
- ca-certificates=2024.2.2=hbcca054_0
- certifi=2024.2.2=pyhd8ed1ab_0
- cffi=1.16.0=py310h2fee648_0
- charset-normalizer=3.3.2=pyhd8ed1ab_0
- colorama=0.4.6=pyhd8ed1ab_0
- conda=24.3.0=py310hff52083_0
- conda-libmamba-solver=23.12.0=pyhd8ed1ab_0
- conda-package-handling=2.2.0=pyh38be061_0
- conda-package-streaming=0.9.0=pyhd8ed1ab_0
- distro=1.8.0=pyhd8ed1ab_0
- fmt=10.2.1=h00ab1b0_0
- icu=73.2=h59595ed_0
- idna=3.6=pyhd8ed1ab_0
- jsonpatch=1.33=pyhd8ed1ab_0
- jsonpointer=2.4=py310hff52083_3
- keyutils=1.6.1=h166bdaf_0
- krb5=1.21.2=h659d440_0
- ld_impl_linux-64=2.40=h41732ed_0
- libarchive=3.7.2=h2aa1ff5_1
- libcurl=8.7.1=hca28451_0
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=hd590300_2
- libffi=3.4.2=h7f98852_5
- libgcc-ng=13.2.0=h807b86a_3
- libgomp=13.2.0=h807b86a_3
- libiconv=1.17=hd590300_2
- libmamba=1.5.8=had39da4_0
- libmambapy=1.5.8=py310h39ff949_0
- libnghttp2=1.58.0=h47da74e_1
- libnsl=2.0.1=hd590300_0
- libsolv=0.7.27=hfc55251_0
- libsqlite=3.44.2=h2797004_0
- libssh2=1.11.0=h0841786_0
- libstdcxx-ng=13.2.0=h7e041cc_3
- libuuid=2.38.1=h0b41bf4_0
- libxml2=2.12.3=h232c23b_0
- libzlib=1.2.13=hd590300_5
- lz4-c=1.9.4=hcb278e6_0
- lzo=2.10=h516909a_1000
- mamba=1.5.8=py310h51d5547_0
- menuinst=2.0.1=py310hff52083_0
- ncurses=6.4=h59595ed_2
- openssl=3.2.1=hd590300_1
- packaging=23.2=pyhd8ed1ab_0
- pip=23.3.2=pyhd8ed1ab_0
- platformdirs=4.1.0=pyhd8ed1ab_0
- pluggy=1.3.0=pyhd8ed1ab_0
- pybind11-abi=4=hd8ed1ab_3
- pycosat=0.6.6=py310h2372a71_0
- pycparser=2.21=pyhd8ed1ab_0
- pysocks=1.7.1=pyha2e5f31_6
- python=3.10.13=hd12c33a_0_cpython
- python_abi=3.10=4_cp310
- readline=8.2=h8228510_1
- reproc=14.2.4.post0=hd590300_1
- reproc-cpp=14.2.4.post0=h59595ed_1
- requests=2.31.0=pyhd8ed1ab_0
- ruamel.yaml=0.18.5=py310h2372a71_0
- ruamel.yaml.clib=0.2.7=py310h2372a71_2
- setuptools=68.2.2=pyhd8ed1ab_0
- tk=8.6.13=noxft_h4845f30_101
- tqdm=4.66.1=pyhd8ed1ab_0
- truststore=0.8.0=pyhd8ed1ab_0
- tzdata=2023c=h71feb2d_0
- urllib3=2.1.0=pyhd8ed1ab_0
- wheel=0.42.0=pyhd8ed1ab_0
- xz=5.2.6=h166bdaf_0
- yaml-cpp=0.8.0=h59595ed_0
- zstandard=0.22.0=py310h1275a96_0
- zstd=1.5.5=hfc55251_0BTW I have seen this problem with several other people's fresh conda installs, so I know it is not just me. |
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Thank you for sharing, gives me something to compare against. Curious, have you tried with |
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If it helps, I'm using the latest miniforge |
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I've just tried with I have now created a Docker-based example to reproduce this bug here. |
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Hiya, today I installed Bactopia with conda on a new computer and have run into what I think is the same problem. ERROR ~ Error executing process > 'BACTOPIA:ANNOTATOR:PROKKA_MODULE (15)' Caused by: |
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The working build on my old laptop has perl v. 5.26.1, whereas the new build has v. 5.34.0. Could that be the issue? Similar to what was seen here bioconda/bioconda-recipes#20459 (comment) |
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@pvanheus and @Kiratrea can you confirm if @pvanheus - if I remove Possible culprit - Perl packages moved from Bioconda to Conda-ForgeIf you are using Two of the packages Circling back, Similar situation if you explicittly ask for the bioconda version At the end of all this I agree with @pvanheus I don't think this is a Bactopia specific issue, but a wider issue, related to I guess, question becomes: Can the Prokka recipe on Bioconda be fixed to allow the usage of |
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Me again! More digging on my end. I was curious why I explicitly pinned Bioperl to 1.7.2, and it was due to this: bioconda/bioconda-recipes#33411 Which was subsequently fixed in bioconda/bioconda-recipes#33805 It looks like my pinning of bioperl to 1.7.2, is now the issue due to the movement of packages from bioconda to conda-forge and Good news though, it should be a simple solution! Just need to unpin bioperl in the module, since the missing Perl package is no longer an issue. Which I have done: f0f3b32 (it is available in my dev build) |
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I installed the development build and everything ran great! Thank you so much for your help! |
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Hello! @rpetit3 I'm a bioinformatics student and I don't know much about programming. Can you help me learn how to install the development build? Thanks! |
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Apologies for the delay @VictorPizarroR Here's the command: |
Description
An attempt to run bactopia with conda package resolution fails because prokka relies on bioperl-1.7.2 which is currently not installable using conda.
Steps to Reproduce
Either (1) run bactopia or (2) directly try and install the dependencies that the
prokkamodule needs. In fact the problem is the same if you simply try and install bioperl-1.7.2.Expected Behavior
A description of what is expected to happen.
Execution Environment
Additional Information
This is strictly a problem with the bioperl recipe and not bactopia. I think the bioperl problem is related to the pinning of bioperl 1.7.2 to perl-bioperl-core 1.007002. This problem is resolved in bioperl 1.7.8.
The prokka module in bactopia is listed as nf-core but it is somewhat diverged from the upstream nf-core module.
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