kwinker commented 4 months ago

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:

faircloth-lab/label/phyluce
conda-forge
bioconda
defaults
default Platform: osx-64 Collecting package metadata (repodata.json): done Solving environment: failed Channels:
faircloth-lab/label/phyluce
conda-forge
bioconda
defaults
default Platform: osx-64 Collecting package metadata (repodata.json): done Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:

package mafft-7.475-hb4d813b_1 is excluded by strict repo priority

(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:

#

bioconda
conda-forge
default
defaults 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.

kwinker commented 4 months ago

Okay -- a solution to a similar issue has appeared here: https://github.com/ContinuumIO/anaconda-issues/issues/13340 Soumya624 commented • "Got the same issue when I was trying to use conda config --set channel_priority strict. But, making it Flexible was solving the issue!"

Trying that myself seems to have enabled complete installation of phyluce, thus:

conda config --set channel_priority flexible conda activate phyluce-1.7.3-x86 conda config --env --set subdir osx-64 conda env update --name phyluce-1.7.3-x86 --file phyluce-1.7.3-py36-macOS-conda.yml --prune

I get seemingly error-free installation feedback and a much longer conda list response:

Channels:

faircloth-lab/label/phyluce
conda-forge
bioconda
defaults
default Platform: osx-64 Collecting package metadata (repodata.json): done Solving environment: done

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: /
#############################################################################################

Note: SPAdes installed through bioconda on MacOS may be somewhat slower than the SPAdes

binaries distributed by the authors at

http://cab.spbu.ru/files/release3.14.1/SPAdes-3.14.1-Darwin.tar.gz

due to unavailability of parallel libstdc++ for the Clang compiler used by bioconda on

MacOS; see https://github.com/ablab/spades/issues/194#issuecomment-523175204

#############################################################################################

done

To activate this environment, use

$ conda activate phyluce-1.7.3-x86

To deactivate an active environment, use

$ conda deactivate

conda list

packages in environment at /Users/melospiza/miniconda3/envs/phyluce-1.7.3-x86:

#

Name Version Build Channel

abyss 1.5.2 boost1.61_5 bioconda amply 0.1.6 pyhd8ed1ab_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge attrs 22.2.0 pyh71513ae_0 conda-forge bcftools 1.11 he8d9d6d_0 bioconda bedtools 2.30.0 h0e31d98_3 bioconda biopython 1.78 py36hfa26744_2 conda-forge brotlipy 0.7.0 py36hfa26744_1001 conda-forge bwa 0.7.17 h45fc8d7_11 bioconda bx-python 0.8.9 py36h4fb836f_2 bioconda bzip2 1.0.8 h10d778d_5 conda-forge c-ares 1.19.1 h0dc2134_0 conda-forge ca-certificates 2023.5.7 h8857fd0_0 conda-forge certifi 2021.5.30 py36h79c6626_0 conda-forge cffi 1.14.6 py36hbc36220_1 conda-forge chardet 4.0.0 py36h79c6626_1 conda-forge coin-or-cbc 2.10.10 he49632c_0 conda-forge coin-or-cgl 0.60.3 h1c2bb20_2 conda-forge coin-or-clp 1.17.7 h79c0eca_0 conda-forge coin-or-osi 0.108.8 hfef9e4d_0 conda-forge coin-or-utils 2.11.9 he494582_0 conda-forge coincbc 2.10.10 0_metapackage conda-forge colorama 0.4.5 pyhd8ed1ab_0 conda-forge commonmark 0.9.1 py_0 conda-forge configargparse 1.5.5 pyhd8ed1ab_0 conda-forge cryptography 35.0.0 py36ha6a00b0_0 conda-forge dataclasses 0.7 pyhe4b4509_6 conda-forge datrie 0.8.2 py36hfa26744_2 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge dendropy 4.5.2 pyh3252c3a_0 bioconda docutils 0.17.1 py36h79c6626_0 conda-forge future 0.18.2 py36h79c6626_3 conda-forge gblocks 0.91b h527b516_2 bioconda gettext 0.21.1 h8a4c099_0 conda-forge gitdb 4.0.10 pyhd8ed1ab_0 conda-forge gitpython 3.1.18 pyhd8ed1ab_0 conda-forge gmp 6.2.1 h2e338ed_0 conda-forge gsl 2.6 h71c5fe9_2 conda-forge htslib 1.11 h422799e_2 bioconda idna 2.10 pyh9f0ad1d_0 conda-forge illumiprocessor 2.10 py_0 faircloth-lab/label/phyluce importlib-metadata 4.8.1 py36h79c6626_0 conda-forge importlib_metadata 4.8.1 hd8ed1ab_1 conda-forge iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge ipython_genutils 0.2.0 pyhd8ed1ab_1 conda-forge jsonschema 4.1.2 pyhd8ed1ab_0 conda-forge jupyter_core 4.8.1 py36h79c6626_0 conda-forge krb5 1.20.1 h0165f36_0 conda-forge lastz 1.0.4 hb4d813b_5 bioconda libblas 3.9.0 17_osx64_openblas conda-forge libcblas 3.9.0 17_osx64_openblas conda-forge libcurl 7.87.0 haf73cf8_0 conda-forge libcxx 16.0.6 hd57cbcb_0 conda-forge libdeflate 1.18 hac1461d_0 conda-forge libedit 3.1.20191231 h0678c8f_2 conda-forge libev 4.33 h10d778d_2 conda-forge libffi 3.4.2 h0d85af4_5 conda-forge libgcc 4.8.5 1 conda-forge libgfortran 5.0.0 11_3_0_h97931a8_32 conda-forge libgfortran5 12.2.0 he409387_32 conda-forge libiconv 1.17 hd75f5a5_2 conda-forge libidn2 2.3.4 hb7f2c08_0 conda-forge liblapack 3.9.0 17_osx64_openblas conda-forge liblapacke 3.9.0 17_osx64_openblas conda-forge libnghttp2 1.51.0 h0dd9d14_0 conda-forge libopenblas 0.3.23 openmp_h429af6e_0 conda-forge libsqlite 3.42.0 h58db7d2_0 conda-forge libssh2 1.10.0 h7535e13_3 conda-forge libunistring 0.9.10 h0d85af4_0 conda-forge libzlib 1.2.13 h87427d6_6 conda-forge llvm-openmp 16.0.6 hff08bdf_0 conda-forge lzo 2.10 h10d778d_1001 conda-forge mafft 7.475 hb4d813b_1 bioconda make 4.3 h22f3db7_1 conda-forge more-itertools 9.1.0 pyhd8ed1ab_0 conda-forge mpi 1.0 openmpi conda-forge muscle 3.8.1551 hb280591_6 bioconda nbformat 5.1.3 pyhd8ed1ab_0 conda-forge ncurses 6.2 h2e338ed_4 conda-forge numpy 1.19.5 py36h08b5fde_2 conda-forge openjdk 11.0.8 hb0a8c7a_0 conda-forge openmpi 4.0.5 h5807002_4 conda-forge openssl 1.1.1u h8a1eda9_0 conda-forge packaging 21.3 pyhd8ed1ab_0 conda-forge pandas 1.1.5 py36h2be6da3_0 conda-forge perl 5.32.1 7_h10d778d_perl5 conda-forge phyluce 1.7.3 py36_0 faircloth-lab/label/phyluce pilon 1.23 hdfd78af_3 bioconda pip 20.0.2 py_2 conda-forge pluggy 0.13.1 py36h79c6626_4 conda-forge psutil 5.8.0 py36hfa26744_1 conda-forge pulp 2.5.1 py36h79c6626_0 conda-forge py 1.11.0 pyh6c4a22f_0 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pygments 2.14.0 pyhd8ed1ab_0 conda-forge pyopenssl 22.0.0 pyhd8ed1ab_1 conda-forge pyparsing 3.1.0 pyhd8ed1ab_0 conda-forge pyrsistent 0.17.3 py36hfa26744_2 conda-forge pysocks 1.7.1 py36h79c6626_3 conda-forge pytest 6.2.2 py36h79c6626_0 conda-forge python 3.6.15 haf480d7_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-lzo 1.12 py36h3f91037_1003 conda-forge python_abi 3.6 2_cp36m conda-forge pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge pyyaml 5.4.1 py36hfa26744_1 conda-forge ratelimiter 1.2.0 pyhd8ed1ab_1003 conda-forge raxml-ng 1.0.1 ha44586f_0 bioconda readline 8.1 h05e3726_0 conda-forge requests 2.25.1 pyhd3deb0d_0 conda-forge rich 9.2.0 py36h79c6626_0 conda-forge samtools 1.11 h725deca_0 bioconda seqtk 1.3 h45fc8d7_6 bioconda setuptools 49.6.0 py36h79c6626_3 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge smmap 3.0.5 pyh44b312d_0 conda-forge snakemake-minimal 5.32.2 py_0 bioconda spades 3.14.1 he641558_1 bioconda sqlite 3.37.0 h23a322b_0 conda-forge tk 8.6.12 h5dbffcc_0 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge toposort 1.7 pyhd8ed1ab_0 conda-forge traitlets 4.3.3 pyhd8ed1ab_2 conda-forge trimal 1.4.1 h85dcccf_9 bioconda trimmomatic 0.39 hdfd78af_2 bioconda typing_extensions 3.10.0.2 pyha770c72_0 conda-forge urllib3 1.26.15 pyhd8ed1ab_0 conda-forge velvet 1.2.10 1 bioconda wget 1.20.1 h33e2efd_0 conda-forge wheel 0.36.2 pyhd3deb0d_0 conda-forge wrapt 1.13.1 py36hfa26744_0 conda-forge xz 5.2.6 h775f41a_0 conda-forge yaml 0.2.5 h0d85af4_2 conda-forge zipp 3.6.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 h87427d6_6 conda-forge

kwinker commented 4 months ago

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)).

brantfaircloth commented 4 months ago

Howdy. Neither Picard nor GATK are included with phyluce any longer because of licensing restrictions that come w/ packaging them up for distribution.

kwinker commented 4 months ago

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.

brantfaircloth commented 4 months ago

You can see if conda will install them for you manually (activate the environment then conda/mamba install gatk & conda/mamba install picard). It looks like you can get up to GATK 3.8 (GATK current version is 4.6). The version of picard available from conda is also the most current version available.

kwinker commented 4 months ago

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.)

faircloth-lab / phyluce

phyluce installation error at the conda env update --name phyluce-1.7.3-x86 ... stage #343

packages in environment at /Users/melospiza/miniconda3/envs/phyluce-1.7.3-x86:

Name Version Build Channel

packages in environment at /Users/melospiza/miniconda3:

Name Version Build Channel

Package Plan

Note: SPAdes installed through bioconda on MacOS may be somewhat slower than the SPAdes

binaries distributed by the authors at

http://cab.spbu.ru/files/release3.14.1/SPAdes-3.14.1-Darwin.tar.gz

due to unavailability of parallel libstdc++ for the Clang compiler used by bioconda on

MacOS; see https://github.com/ablab/spades/issues/194#issuecomment-523175204

To activate this environment, use

$ conda activate phyluce-1.7.3-x86

To deactivate an active environment, use

$ conda deactivate

packages in environment at /Users/melospiza/miniconda3/envs/phyluce-1.7.3-x86:

Name Version Build Channel