ずっとPythonは素のPython3をつかっている。
Anacondaはいっとき手を出した事はあるが、conda以外のpipでインストールしたライブラリとの折り合いが悪く、結局アンインストールして今に至る。
しかし素のPython3では依存関係がうまく構築できない案件がやはり出てくるので、pyenvで共存を図ることにしたい。
homebrewでpyenvとpyenv-virtualenvをインストールする。
そのために
$ brew update Updated 4 taps (qmk/qmk, homebrew/core, homebrew/cask and brewsci/bio). ==> New Formulae ・・・・・ You have 132 outdated formulae and 2 outdated casks installed. You can upgrade them with brew upgrade or list them with brew outdated. $ brew upgrade ==> Upgrading 132 outdated packages: ・・・・・ ==> `brew cleanup` has not been run in the last 30 days, running now... Disable this behaviour by setting HOMEBREW_NO_INSTALL_CLEANUP. Hide these hints with HOMEBREW_NO_ENV_HINTS (see `man brew`). Removing: /usr/local/Cellar/openssl@1.1/1.1.1k... (8,071 files, 18.5MB) Error: Permission denied @ apply2files - /usr/local/lib/docker/cli-plugins
久しぶりにMacのHomebrewをアップデートしたら（もしかしたらCatarinaにアップデートして初めて？）いきなりエラーでつまづく。
$ sudo chown -R $(whoami) $(brew --prefix)/* $ brew upgrade ==> Upgrading 130 outdated packages: ・・・・・ Warning: Your Xcode (11.3.1) is outdated. Please update to Xcode 12.4 (or delete it). Xcode can be updated from the App Store. ・・・・・ ==> Caveats `osxfuse` has been succeeded by `macfuse` as of version 4.0.0. To update to a newer version, do: brew uninstall osxfuse brew install macfuse osxfuse requires a kernel extension to work. If the installation fails, retry after you enable it in: System Preferences → Security & Privacy → General For more information, refer to vendor documentation or this Apple Technical Note: https://developer.apple.com/library/content/technotes/tn2459/_index.html You must reboot for the installation of osxfuse to take effect. ・・・・・ Error: emacs: It seems the App source '/Applications/Emacs.app' is not there.
なにやら不穏なCaveatsやWarningがたびたび出て、あげくまた別のエラーで止まる。
Emacsなんてそもそも入れてないはずなんだけどなあ。
$ brew reinstall emacs --cask --no-quarantine ==> Downloading https://emacsformacosx.com/emacs-builds/Emacs-28.1-4-universal.d Already downloaded: /Users/kuro/Library/Caches/Homebrew/downloads/96cf5c42fb25db0b78be33651afe4cd8fc82097a0a81e10b4125a5d2831a125d--Emacs-28.1-4-universal.dmg ==> Uninstalling Cask emacs ==> Purging files for version 25.2 of Cask emacs ==> Installing Cask emacs Warning: macOS's Gatekeeper has been disabled for this Cask ==> Moving App 'Emacs.app' to '/Applications/Emacs.app' ==> Linking Binary 'Emacs' to '/usr/local/bin/emacs' ==> Linking Binary 'ebrowse' to '/usr/local/bin/ebrowse' ==> Linking Binary 'emacsclient' to '/usr/local/bin/emacsclient' ==> Linking Binary 'etags' to '/usr/local/bin/etags' ==> Linking Manpage 'ebrowse.1.gz' to '/usr/local/share/man/man1/ebrowse.1.gz' ==> Linking Manpage 'emacs.1.gz' to '/usr/local/share/man/man1/emacs.1.gz' ==> Linking Manpage 'emacsclient.1.gz' to '/usr/local/share/man/man1/emacsclient ==> Linking Manpage 'etags.1.gz' to '/usr/local/share/man/man1/etags.1.gz' 🍺 emacs was successfully installed! $ brew upgrade Running `brew update --preinstall`... ==> Auto-updated Homebrew! Updated 1 tap (homebrew/cask). ==> New Casks bili-downloader ==> Updated Casks Updated 2 casks.
なんかわからんがようやくbrew upgradeまで完了。
$ brew install pyenv pyenv-virtualenv $ nano .bashrc
# pyenv
PYENV_ROOT=~/.pyenv
export PATH=$PYENV_ROOT/bin:$PATH
eval "$(pyenv init -)"
eval "$(pyenv virtualenv-init -)"
# brew doctor
alias brew="env PATH=${PATH/\/Users\/${USER}\/\.pyenv\/shims:/} brew"を.bashrcに追記
$ source .bashrc
$ pyenv install anaconda3-5.3.1
Downloading Anaconda3-5.3.1-MacOSX-x86_64.sh.sh...
-> https://repo.continuum.io/archive/Anaconda3-5.3.1-MacOSX-x86_64.sh
Installing Anaconda3-5.3.1-MacOSX-x86_64.sh...
Installed Anaconda3-5.3.1-MacOSX-x86_64.sh to /Users/kkuro/.pyenv/versions/anaconda3-5.3.1
$ pyenv virtualenv anaconda3-5.3.1 anac1
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.5.11
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
・・・・・
# To activate this environment, use:
# > source activate anac1
#
# To deactivate an active environment, use:
# > source deactivate
#
Looking in links: /var/folders/sf/3lk5x37135586w0jgqyjq_yc0000gn/T/tmpwy8czazq
Requirement already satisfied: setuptools in /Users/kuro/.pyenv/versions/anaconda3-5.3.1/envs/anac1/lib/python3.10/site-packages (61.2.0)
Requirement already satisfied: pip in /Users/kuro/.pyenv/versions/anaconda3-5.3.1/envs/anac1/lib/python3.10/site-packages (21.2.4)
$ source activate anac1
pyenv-virtualenv: activate anac1
pyenv-virtualenv: prompt changing will be removed from future release. configure `export PYENV_VIRTUALENV_DISABLE_PROMPT=1' to simulate the behavior.
$ source deactivate
pyenv-virtualenv: deactivate anaconda3-5.3.1/envs/anac1anac1という名前で仮想環境を作る。
ホームディレクトリにanac1というディレクトリを作り、仮想環境はその中だけで動作させる設定にしたい。
$ mkdir anac1 $ cd anac1 $ pyenv versions * system (set by /Users/kkuro/.pyenv/version) anac1 anaconda3-5.3.1 anaconda3-5.3.1/envs/anac1 $ pyenv local anac1
ここでプロンプトが
kuro-Mac:anac1 kuro$
から
(anac1) kuro-Mac:anac1 kuro$
というように頭に(anac1)がつく。
(anac1) kuro-Mac:anac1 kuro$ pyenv versions system * anac1 (set by /Users/kuro/anac1/.python-version) anaconda3-5.3.1 anaconda3-5.3.1/envs/anac1 (anac1) kuro-Mac:anac1 kuro$ cd kuro-Mac:~ kuro$ pyenv versions * system (set by /Users/kuro/.pyenv/version) anac1 anaconda3-5.3.1 anaconda3-5.3.1/envs/anac1
このようにanac1ディレクトリから出ると素のPython3環境に自動的に戻る。
さて、Anacondaを入れることにした要因のETE Toolkitをインストールしておこう。
先ほど作成したanac1ディレクトリに入り
$ conda create -n ete3 python=3
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.5.11
latest version: 4.12.0
Please update conda by running
$ conda update -n base -c defaults conda
・・・・・
#
# To activate this environment, use:
# > source activate ete3
#
# To deactivate an active environment, use:
# > source deactivate
#
$ conda activate ete3
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
If your shell is Bash or a Bourne variant, enable conda for the current user with
$ echo ". /Users/kuro/.pyenv/versions/anaconda3-5.3.1/etc/profile.d/conda.sh" >> ~/.bash_profile
・・・・・早速エラーが出る。言われたように対応して
$ echo ". /Users/kuro/.pyenv/versions/anaconda3-5.3.1/etc/profile.d/conda.sh" >> ~/.bash_profile $ source ../.bash_profile $ conda activate ete3
そっけなく
(ete3) (anac1) kuro-Mac:anac1 kurovmax@gmail.com$
とプロンプトが変わり、
$ conda install -c etetoolkit ete3 ete_toolchain
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.5.11
latest version: 4.12.0
・・・・・
Downloading and Extracting Packages
gettext-0.21.0 | 3.4 MB | ##################################### | 100%
pip-21.2.2 | 2.1 MB | ##################################### | 100%
mafft-6.861 | 4.8 MB | ##################################### | 100%
fasttree-2.1 | 278 KB | ##################################### | 100%
mkl_fft-1.3.0 | 175 KB | ##################################### | 100%
expat-2.4.4 | 145 KB | ##################################### | 100%
setuptools-58.0.4 | 970 KB | ##################################### | 100%
mkl_random-1.1.1 | 334 KB | ##################################### | 100%
certifi-2021.5.30 | 141 KB | ##################################### | 100%
numpy-base-1.19.2 | 5.0 MB | ##################################### | 100%
lxml-4.6.3 | 1.3 MB | ##################################### | 100%
sip-4.19.8 | 252 KB | ##################################### | 100%
libiconv-1.16 | 1.3 MB | ##################################### | 100%
kalign-2.03 | 261 KB | ##################################### | 100%
scipy-1.5.2 | 17.3 MB | ##################################### | 100%
pcre-8.45 | 221 KB | ##################################### | 100%
ete3-3.1.2 | 2.1 MB | ##################################### | 100%
argtable2-2.13 | 2.7 MB | ##################################### | 100%
dbus-1.13.18 | 550 KB | ##################################### | 100%
paml-4.8 | 7.0 MB | ##################################### | 100%
muscle-3.8.31 | 1.8 MB | ##################################### | 100%
libxslt-1.1.34 | 534 KB | ##################################### | 100%
mkl-service-2.3.0 | 45 KB | ##################################### | 100%
pyqt-5.9.2 | 4.4 MB | ##################################### | 100%
phylobayes-4.1c | 27.3 MB | ##################################### | 100%
glib-2.69.1 | 3.3 MB | ##################################### | 100%
phyml-20160115.patch | 3.9 MB | ##################################### | 100%
raxml-8.2.11 | 10.4 MB | ##################################### | 100%
mkl-2019.4 | 155.2 MB | ##################################### | 100%
dialigntx-1.0.2 | 2.4 MB | ##################################### | 100%
libgcc-4.8.5 | 302 KB | ##################################### | 100%
pmodeltest-1.4 | 729 KB | ##################################### | 100%
t_coffee-11.00 | 10.5 MB | ##################################### | 100%
slr-1.4.3 | 862 KB | ##################################### | 100%
iqtree-1.5.5 | 11.2 MB | ##################################### | 100%
clustalo-1.2.4 | 1.4 MB | ##################################### | 100%
python-3.6.13 | 20.3 MB | ##################################### | 100%
ete_toolchain-3.0.0 | 4 KB | ##################################### | 100%
llvm-openmp-12.0.0 | 300 KB | ##################################### | 100%
trimal-1.4 | 1.4 MB | ##################################### | 100%
intel-openmp-2022.0. | 1.2 MB | ##################################### | 100%
numpy-1.19.2 | 20 KB | ##################################### | 100%
libxml2-2.9.12 | 1.2 MB | ##################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
$ ete3 version
3.1.2 Tools path: /Users/kuro/.pyenv/versions/anaconda3-5.3.1/envs/ete3/lib/python3.6/site-packages/ete3-3.1.2-py3.7.egg/ete3/tools
$ ete3 build check
Current Toolchain path: /Users/kuro/.pyenv/versions/anaconda3-5.3.1/envs/ete3/bin/ete3_apps/bin
Current Toolchain version: unknown
clustalo: MISSING
codeml: OK - AAML in paml version 4.8a, July 2014
Dialign-tx not supported in OS X
fasttree: OK - Usage for FastTree version 2.1.8 Double precision (No SSE3), OpenMP (1 threads):
iqtree: OK - IQ-TREE multicore version 1.5.5 for Mac OS X 64-bit built Jun 2 2017
kalign: OK - Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann
mafft: OK - MAFFT v6.861b (2011/09/24)
muscle: OK - MUSCLE v3.8.31 by Robert C. Edgar
phyml: OK - . This is PhyML version 20160115.
pmodeltest: OK - pmodeltest.py v1.4
raxml: OK - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
raxml-pthreads: OK - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
readal: OK - readAl v1.4.rev6 build[2012-02-02]
slr: OK - # SLR "Sitewise Likelihood Ratio" selection detection program. Version 1.4.3
statal: OK - statAl v1.4.rev6 build[2012-02-02]
tcoffee: OK - PROGRAM: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477)
trimal: OK - trimAl v1.4.rev6 build[2012-02-02]
WARNING: 1 external tools seem to be missing or unfunctional
Install using conda (recomended):
conda install -c etetoolkit ete3_external_apps
or manually compile by running:
ete3 upgrade-external-toolsインストールできたのか？。
clustaloが入ってないよ、と言っている気がする。
Clustal Omega - fast, accurate, scalable multiple sequence alignment for proteins
ここでMac用バイナリをダウンロードしてきて名前をclustaloに変える。そして
/Users/kuro/.pyenv/versions/anaconda3-5.3.1/envs/ete3/bin/ete3_apps/bin/
に移動させてchmod 755としてやれば
o$ ete3 build check
Current Toolchain path: /Users/kuro/.pyenv/versions/anaconda3-5.3.1/envs/ete3/bin/ete3_apps/bin
Current Toolchain version: unknown
clustalo: OK - 1.2.3
codeml: OK - AAML in paml version 4.8a, July 2014
Dialign-tx not supported in OS X
fasttree: OK - Usage for FastTree version 2.1.8 Double precision (No SSE3), OpenMP (1 threads):
iqtree: OK - IQ-TREE multicore version 1.5.5 for Mac OS X 64-bit built Jun 2 2017
kalign: OK - Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann
mafft: OK - MAFFT v6.861b (2011/09/24)
muscle: OK - MUSCLE v3.8.31 by Robert C. Edgar
phyml: OK - . This is PhyML version 20160115.
pmodeltest: OK - pmodeltest.py v1.4
raxml: OK - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
raxml-pthreads: OK - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
readal: OK - readAl v1.4.rev6 build[2012-02-02]
slr: OK - # SLR "Sitewise Likelihood Ratio" selection detection program. Version 1.4.3
statal: OK - statAl v1.4.rev6 build[2012-02-02]
tcoffee: OK - PROGRAM: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477)
trimal: OK - trimAl v1.4.rev6 build[2012-02-02]これでいいですね。DialignはMacでは使えないらしいのでどうにもならん。
とまあインストールできたように見えるんだけど、どうしたわけか動かないんだよなETE3 toolkit。バカバカしくなってきたから撤退。
