phyluce installation error at the conda env update --name phyluce-1.7.3-x86 ... stage #343
Comments
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Okay -- a solution to a similar issue has appeared here: ContinuumIO/anaconda-issues#13340 Trying that myself seems to have enabled complete installation of phyluce, thus: conda config --set channel_priority flexible I get seemingly error-free installation feedback and a much longer conda list response: Channels:
Downloading and Extracting Packages: Preparing transaction: done Note: SPAdes installed through bioconda on MacOS may be somewhat slower than the SPAdesbinaries distributed by the authors athttp://cab.spbu.ru/files/release3.14.1/SPAdes-3.14.1-Darwin.tar.gzdue to unavailability of parallel libstdc++ for the Clang compiler used by bioconda onMacOS; see ablab/spades#194 (comment)############################################################################################# done To activate this environment, use$ conda activate phyluce-1.7.3-x86To deactivate an active environment, use$ conda deactivateconda list packages in environment at /Users/melospiza/miniconda3/envs/phyluce-1.7.3-x86:Name Version Build Channelabyss 1.5.2 boost1.61_5 bioconda |
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Ahh, but the full problem is not resolved. Unlike a functional installation, this one lacks at least two alias files that I see with a successful installation: gatk and picard. So there does appear to be an installation issue even though it looks like it is successful. The failure is revealed when I call picard and gatk in the phyluce environment and get command not found. (They are available in (base)). |
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Howdy. Neither Picard nor GATK are included with phyluce any longer because of licensing restrictions that come w/ packaging them up for distribution. |
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Thanks, Brant. I wondered. But how do we set up the phyluce environment so picard and gatk get called from within it? Right now, I need to step back to (base) to use them. |
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You can see if conda will install them for you manually (activate the environment then |
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Yes, thanks, I did that, but I can't access them once I am in the phyluce environment, as I used to be able to do. (Also, I was able to upgrade to >gatk4, but don't have my notes at hand on that.) |
Running an M2 Max on a Mac Studio with Sonoma 14.5, and installed Miniconda3-py39_24.4.0-0-MacOSX-arm64.sh
At the command
conda env update --name phyluce-1.7.3-x86 --file phyluce-1.7.3-py36-macOS-conda.yml --prune
it generates a LibMambaUnsatisfiableError with the mafft package and doesn't install other key packages (e.g., picard, samtools).
Here are the screen details:
(base) melospiza@Melospiza2024s-Mac-Studio ~ % conda activate phyluce-1.7.3-x86
(phyluce-1.7.3-x86) melospiza@Melospiza2024s-Mac-Studio ~ % conda config --env --set subdir osx-64
(phyluce-1.7.3-x86) melospiza@Melospiza2024s-Mac-Studio ~ % conda env update --name phyluce-1.7.3-x86 --file phyluce-1.7.3-py36-macOS-conda.yml --prune
Channels:
Platform: osx-64
Collecting package metadata (repodata.json): done
Solving environment: failed
Channels:
Platform: osx-64
Collecting package metadata (repodata.json): done
Solving environment: failed
LibMambaUnsatisfiableError: Encountered problems while solving:
(phyluce-1.7.3-x86) melospiza@Melospiza2024s-Mac-Studio ~ % conda list
packages in environment at /Users/melospiza/miniconda3/envs/phyluce-1.7.3-x86:
Name Version Build Channel
ca-certificates 2024.6.2 h8857fd0_0 conda-forge
libcxx 17.0.6 h8d2f0da_1 conda-forge
libffi 3.4.2 h0d85af4_5 conda-forge
libsqlite 3.46.0 h1b8f9f3_0 conda-forge
libzlib 1.3.1 h87427d6_1 conda-forge
ncurses 6.5 h5846eda_0 conda-forge
openssl 1.1.1w h8a1eda9_0 conda-forge
pip 21.3.1 pyhd8ed1ab_0 conda-forge
python 3.6.15 haf480d7_0_cpython conda-forge
python_abi 3.6 2_cp36m conda-forge
readline 8.2 h9e318b2_1 conda-forge
setuptools 58.0.4 py36h79c6626_2 conda-forge
sqlite 3.46.0 h28673e1_0 conda-forge
tk 8.6.13 h1abcd95_1 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h775f41a_0 conda-forge
(phyluce-1.7.3-x86) melospiza@Melospiza2024s-Mac-Studio ~ % conda deactivate
(base) melospiza@Melospiza2024s-Mac-Studio ~ % conda list
packages in environment at /Users/melospiza/miniconda3:
Name Version Build Channel
anaconda-anon-usage 0.4.4 py39hd6b623d_100
archspec 0.2.3 pyhd3eb1b0_0
boltons 23.0.0 py39hca03da5_0
brotli-python 1.0.9 py39h313beb8_8
bzip2 1.0.8 h80987f9_6
c-ares 1.19.1 h80987f9_0
ca-certificates 2024.3.11 hca03da5_0
certifi 2024.2.2 py39hca03da5_0
cffi 1.16.0 py39h80987f9_1
charset-normalizer 2.0.4 pyhd3eb1b0_0
conda 24.4.0 py39hca03da5_0
conda-content-trust 0.2.0 py39hca03da5_1
conda-libmamba-solver 24.1.0 pyhd3eb1b0_0
conda-package-handling 2.2.0 py39hca03da5_1
conda-package-streaming 0.9.0 py39hca03da5_0
cryptography 42.0.5 py39hd4332d6_1
distro 1.9.0 py39hca03da5_0
fmt 9.1.0 h48ca7d4_1
icu 73.1 h313beb8_0
idna 3.7 py39hca03da5_0
jsonpatch 1.33 py39hca03da5_1
jsonpointer 2.1 pyhd3eb1b0_0
krb5 1.20.1 hf3e1bf2_1
libarchive 3.6.2 h62fee54_3
libcurl 8.7.1 h3e2b118_0
libcxx 14.0.6 h848a8c0_0
libedit 3.1.20230828 h80987f9_0
libev 4.33 h1a28f6b_1
libffi 3.4.4 hca03da5_1
libiconv 1.16 h80987f9_3
libmamba 1.5.8 haeffa04_2
libmambapy 1.5.8 py39h1c5506f_2
libnghttp2 1.57.0 h62f6fdd_0
libsolv 0.7.24 h514c7bf_1
libssh2 1.11.0 h3e2b118_0
libxml2 2.10.4 h0b34f26_2
lz4-c 1.9.4 h313beb8_1
menuinst 2.0.2 py39hca03da5_1
ncurses 6.4 h313beb8_0
openssl 3.0.13 h1a28f6b_1
packaging 23.2 py39hca03da5_0
pcre2 10.42 hb066dcc_1
pip 24.0 py39hca03da5_0
platformdirs 3.10.0 py39hca03da5_0
pluggy 1.0.0 py39hca03da5_1
pybind11-abi 4 hd3eb1b0_1
pycosat 0.6.6 py39h80987f9_1
pycparser 2.21 pyhd3eb1b0_0
pysocks 1.7.1 py39hca03da5_0
python 3.9.19 hb885b13_1
python.app 3 py39h1a28f6b_0
readline 8.2 h1a28f6b_0
reproc 14.2.4 h313beb8_2
reproc-cpp 14.2.4 h313beb8_2
requests 2.31.0 py39hca03da5_1
ruamel.yaml 0.17.21 py39h1a28f6b_0
ruamel.yaml.clib 0.2.6 py39h1a28f6b_1
setuptools 69.5.1 py39hca03da5_0
sqlite 3.45.3 h80987f9_0
tk 8.6.14 h6ba3021_0
tqdm 4.66.2 py39h33ce5c2_0
tzdata 2024a h04d1e81_0
urllib3 2.1.0 py39hca03da5_1
wheel 0.43.0 py39hca03da5_0
xz 5.4.6 h80987f9_1
yaml-cpp 0.8.0 h313beb8_1
zlib 1.2.13 h18a0788_1
zstandard 0.22.0 py39h1a4646a_0
zstd 1.5.5 hd90d995_2
(base) melospiza@Melospiza2024s-Mac-Studio ~ % conda install -c bioconda gatk4
Channels:
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: done
Package Plan
environment location: /Users/melospiza/miniconda3
added / updated specs:
- gatk4
...
Any ideas or suggestions welcome!
Best, K.
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