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CGATOxford / UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets
MIT License
481 stars 190 forks source link

On Mac 11.4, four different errors following homebrew procedure #486

Closed bgphd closed 1 year ago

bgphd commented 3 years ago

Hello,

1) pysam version requested for homebrew can't be installed. 2) homebrew doesn't recognize specific pysam requested 3) gcc package 4.8 requested by homebrew doesn't currently exist 4) conda installs on mac are also problemmatic

1) pysam version requested for homebrew can't be installed.

(base) Berts-MacBook-Pro:normal_fq bgold$ 
(base) Berts-MacBook-Pro:normal_fq bgold$ pip install pysam==0.8.4
Collecting pysam==0.8.4
  Downloading pysam-0.8.4.tar.gz (1.7 MB)
     |████████████████████████████████| 1.7 MB 3.7 MB/s 
Building wheels for collected packages: pysam
  Building wheel for pysam (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/local/Caskroom/miniconda/base/bin/python3.8 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/lv/qpv6ld3j1qz_rnqq8b70fybw0000gn/T/pip-install-_scvr12n/pysam_c6fde281fa20449ab306d284e8181649/setup.py'"'"'; __file__='"'"'/private/var/folders/lv/qpv6ld3j1qz_rnqq8b70fybw0000gn/T/pip-install-_scvr12n/pysam_c6fde281fa20449ab306d284e8181649/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/lv/qpv6ld3j1qz_rnqq8b70fybw0000gn/T/pip-wheel-3nz5f8q_
       cwd: /private/var/folders/lv/qpv6ld3j1qz_rnqq8b70fybw0000gn/T/pip-install-_scvr12n/pysam_c6fde281fa20449ab306d284e8181649/
  Complete output (213 lines):

`

2) homebrew doesn't recognize specific pysam requested

``

(base) Berts-MacBook-Pro:normal_fq bgold$ brew install pysam==0.8.4
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 4 taps (homebrew/core, homebrew/cask, homebrew/services and brewsci/bio).
==> New Formulae
alda                           darglint                       hubble                         notcurses                      pydocstyle                     umple
alerter                        doc8                           i2c-tools                      ns-3                           python-launcher                wildmidi
apt                            docuum                         influxdb-cli                   openliberty-jakartaee8         rsc_2fa                        xsel
bash_unit                      fanyi                          licensefinder                  openliberty-microprofile4      slirp4netns                    zet
bupstash                       firefoxpwa                     linux-headers@4.15             openliberty-webprofile8        sql-lint
conmon                         fuse-overlayfs                 macos-term-size                pari-elldata                   stylua
==> Updated Formulae
Updated 1565 formulae.
==> Renamed Formulae
envoy@1.17 -> envoy@1.18             linux-headers -> linux-headers@4.4   parallelstl -> onedpl                wxmac -> wxwidgets                   wxmac@3.0 -> wxwidgets@3.0
==> Deleted Formulae
giter8                                                        terraform-provisioner-ansible                                 tj
==> New Casks
8x8-work                  diagnostics               gosign                    kdocs                     odbc-manager              transfer                  vsdx-annotator
betterdiscord-installer   disk-expert               guilded                   maccleaner-pro            pktriot                   trezor-suite              vym
blackhole-64ch            duplicate-file-finder     hush                      memory-cleaner            shottr                    ubports-installer         wezterm
clock-signal              fluent-reader             jiohome                   midi-router-client        touch-portal              vsd-viewer                wifi-explorer-pro
==> Updated Casks
Updated 799 casks.
==> Deleted Casks
3cxphone                             adobe-lens-profile-creator           beautune                             caramba-switcher                     superbeam
adafruit-arduino                     baiducloud                           blue-jeans-browser-plugin            pdftotext

Warning: No available formula or cask with the name "pysam==0.8.4".
==> Searching for similarly named formulae...
Error: No similarly named formulae found.
==> Searching for a previously deleted formula (in the last month)...
Error: No previously deleted formula found.
==> Searching taps on GitHub...
Error: No formulae found in taps.

3) gcc package 4.8 requested by homebrew doesn't currently exist** NB: Installed 4.9 instead, but plenty of problems with that.

(base) Berts-MacBook-Pro:normal_fq bgold$ brew install gcc48
Warning: No available formula or cask with the name "gcc48". Did you mean gcc@8, gcc, gcc@4.9, gcc@9, gcc@7, gcc@6 or gcc@5?
==> Searching for similarly named formulae...
These similarly named formulae were found:
gcc@8                     gcc ✔                     gcc@4.9                   gcc@9                     gcc@7                     gcc@6                     gcc@5
To install one of them, run (for example):
  brew install gcc@8
==> Searching for a previously deleted formula (in the last month)...
Error: No previously deleted formula found.
==> Searching taps on GitHub...
Error: No formulae found in taps.
(base) Berts-MacBook-Pro:normal_fq bgold$ brew install gcc@4.9
Warning: gcc@4.9 has been deprecated because it is deprecated upstream!

4) conda installs on mac are also problemmatic

(base) Berts-MacBook-Pro:normal_fq bgold$ conda install umi_tools     
Collecting package metadata (current_repodata.json): done
Solving environment: done

#Package Plan# 

  environment location: /usr/local/Caskroom/miniconda/base

  added / updated specs:
    - umi_tools

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    umi_tools-1.1.2            |   py38h68004ad_0         136 KB  bioconda
    ------------------------------------------------------------
                                           Total:         136 KB

The following packages will be UPDATED:

  umi_tools                            1.1.1-py38h68004ad_2 --> 1.1.2-py38h68004ad_0

The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    pkgs/main::ca-certificates-2021.7.5-h~ --> conda-forge::ca-certificates-2021.5.30-h033912b_0

Proceed ([y]/n)? y

Downloading and Extracting Packages
umi_tools-1.1.2      | 136 KB    | ############################################################################################################################################# | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(699): An error occurred while uninstalling package 'bioconda/osx-64::umi_tools-1.1.1-py38h68004ad_2'.
Rolling back transaction: done

[Errno 13] Permission denied: '/usr/local/Caskroom/miniconda/base/lib/python3.8/site-packages/umi_tools-1.1.1.dist-info/INSTALLER' -> '/usr/local/Caskroom/miniconda/base/lib/python3.8/site-packages/umi_tools-1.1.1.dist-info/INSTALLER.c~'
()
IanSudbery commented 3 years ago

Hi, Sorry, I was away when this came in. Unfortunately, our instructions for installing of OSX havn't been updated in a long time.

Unfortunately I don't have access to a Mac in order to try things.

I would begin by just trying to install umi_tools from pip directly pip install umi_tools=1.1.2. Hopefully in the meantime, since the last update, things will have been sorted sufficiently that this will just work. If now, you should probably try more modern version of both gcc and psyam. I don't know which Mac version of gcc is required, but pysam 0.16 should work fine.

Your conda problem look to be because you are installing into a system wide base environment, but don't have the permissions. You could try it with sudo (i.e. sudo conda install umi_tools), or you could create an environment, and install into there (conda create -n umi_tools umi_tools; source activate umi_tools)

Hope this helps.

IanSudbery commented 3 years ago

Did you have any luck with this?