Update biscuit versions for run and hosts#26866
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| - zlib | ||
| - ncurses | ||
| - libcurl | ||
| - zlib >=1.2.11 |
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This should not be needed? Can you describe why you add this lower-pins?
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Thank you for reviewing!
And yes, I need it to work with samtools 1.9, and that's what helped me when I tried locally (with conda --use-local)
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@bgruening for context see: nf-core/methylseq#186 (comment) (we're trying to get this package to work in a fairly large environment that needs to run Samtools v1.9).
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Sorry, not good times here.
I don't think this is the correct solution. Those libraries are pinned globally. This means we set for all compiled packages a zlib version. And if we upgrade the zlib version we recompile all packages (assuming ABI instability etc).
So it should never be needed to pin zlib to a different version and could have a bad impact on your environment.
Can you descripe maybe the underlying problem that you want to solve. I hope we find a better solution :)
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Yes, thanks @bgruening
When using samtools 1.9 in the environment.yml file, the biscuit 0.3.16 default build number is 0.
When using samtools 1.10 in the environment.yml file, the biscuit default build is 3.
So I need that the default build for samtools 1.9 would be biscuit 0.3.16 build 3.
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why can you not specify everything in your environment.yml file, including the build number?
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Because then I get a conflict:
The environment.yml file:
name: nf-core-methylseq-1.5
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- bioconda::htslib=1.9
- bioconda::samtools=1.9
- bioconda::biscuit=0.3.16.20200420=h2b0c03c_3
Output for conda env create -f environment.yml:
Collecting package metadata (repodata.json): done
Solving environment: -
Found conflicts! Looking for incompatible packages. failed
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 htslib conflicts for:
bioconda::htslib=1.9
bioconda|bioconda::htslib=1.9
bioconda::samtools=1.9 -> htslib[version='>=1.9,<1.10.0a0']
Package _libgcc_mutex conflicts for:
bioconda::biscuit==0.3.16.20200420=h2b0c03c_3 -> libgcc-ng[version='>=7.5.0'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main']
bioconda::htslib=1.9 -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main']
bioconda::samtools=1.9 -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main']
Package ncurses conflicts for:
bioconda::biscuit==0.3.16.20200420=h2b0c03c_3 -> ncurses[version='>=6.2,<6.3.0a0']
bioconda::samtools=1.9 -> ncurses[version='>=5.9,<5.10.0a0|>=6.1,<6.2.0a0']
Package libgcc-ng conflicts for:
bioconda::biscuit==0.3.16.20200420=h2b0c03c_3 -> libgcc-ng[version='>=7.5.0']
bioconda::biscuit==0.3.16.20200420=h2b0c03c_3 -> libcurl[version='>=7.71.1,<8.0a0'] -> libgcc-ng[version='>=4.9|>=7.3.0|>=9.3.0|>=7.2.0']
If I use the same environment.yml file, but without specifying the build number, the environment is created OK, but when running conda list inside the environment, I get:
# packages in environment at /path/miniconda3/envs/check_biscuit:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
biscuit 0.3.16.20200420 h802ef42_1 bioconda
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.17.1 h7f98852_1 conda-forge
ca-certificates 2020.12.5 ha878542_0 conda-forge
curl 7.75.0 h979ede3_0 conda-forge
htslib 1.9 h244ad75_9 bioconda
krb5 1.17.2 h926e7f8_0 conda-forge
libcurl 7.75.0 hc4aaa36_0 conda-forge
libdeflate 1.3 h516909a_0 conda-forge
libedit 3.1.20191231 h46ee950_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libgcc-ng 9.3.0 h2828fa1_18 conda-forge
libgomp 9.3.0 h2828fa1_18 conda-forge
libnghttp2 1.43.0 h812cca2_0 conda-forge
libssh2 1.9.0 hab1572f_5 conda-forge
libstdcxx-ng 9.3.0 h6de172a_18 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
openssl 1.1.1j h7f98852_0 conda-forge
samtools 1.9 h10a08f8_12 bioconda
tk 8.6.10 h21135ba_1 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zlib 1.2.11 h516909a_1010 conda-forge
This means that the default biscuit build is 1, and I want it to be 3
And as @ewels said above:
we're trying to get this package to work in a fairly large environment that needs to run Samtools v1.9
3 participants
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