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Keep conda from constricting your brew installs

Sander W. van der Laan edited this page Oct 19, 2022 · 1 revision

Now that you have conda in combination with brew you will get the below message if you run brew doctor.

brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and which additional flags to use when
compiling and linking.

Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew-provided
script of the same name. We found the following "config" scripts:
  /Users/username/anaconda3/bin/icu-config
  /Users/username/anaconda3/bin/krb5-config
  /Users/username/anaconda3/bin/freetype-config
  /Users/username/anaconda3/bin/xslt-config
  /Users/username/anaconda3/bin/libpng16-config
  /Users/username/anaconda3/bin/python3.7-config
  /Users/username/anaconda3/bin/libpng-config
  /Users/username/anaconda3/bin/xml2-config
  /Users/username/anaconda3/bin/python3.7m-config
  /Users/username/anaconda3/bin/python3-config
  /Users/username/anaconda3/bin/curl-config
  /Users/username/anaconda3/bin/ncursesw6-config
  /Users/username/anaconda3/bin/pcre-config

This could be a problem, or just a nuissance. You can change this.

You can add the lines below to your .bashrc file.

open -a BBEdit ~/.bashrc

(Or use another text-editor).

export SANS_ANACONDA="/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin"

# added by Anaconda3 4.4.0 installer

export PATH="/Users/username/anaconda3/bin:$SANS_ANACONDA"

alias perseus="export PATH="\$SANS_ANACONDA" && echo Medusa decapitated."
alias medusa="export PATH="/Users/username/anaconda3/bin:\$SANS_ANACONDA" && echo Perseus defeated."

brew () {
  perseus
  command brew "$@"
  medusa
}

Overview

Welcome to slideToolKit

Manual

Introduction
General instructions

slideToolKit scripts

slide2Tiles
slideAppend.sh
slideAppendGCT.sh
slideConvert
slideDirectory
slideDupIdentify.py
slideEMask
slideEntropySegmentation.py
slideExtract.py
slideExtractTiles.py
slideInfo
slideInfo.py
slideJobChecker
slideLookup
slideMacro
slideMacro.py
slideMask
slideNormalize
slideRename
slideRename.py
slideThumb
slideThumb.py

slideQuantify v1

slideQuantify_v1
slideQuantify_v1_1_expresshist_mask.sh
slideQuantify_v1_2_expresshist_tile.sh
slideQuantify_v1_3_tile_normalizing.sh
slideQuantify_v1_4_cellprofiler.sh
slideQuantify_v1_5_wrapup.sh

slideQuantify v2

slideQuantify_v2
slideQuantify_v2_1_entropy_segmentation.sh
slideQuantify_v2_2_extract_tiles.sh
slideQuantify_v2_3_tile_normalizing.sh
slideQuantify_v2_4_cellprofiler.sh
slideQuantify_v2_5_wrapup.sh

slideQuantifyOSX

slideQuantifyOSX
slideQuantify_cellprofiler.sh
slideQuantify_mask.sh
slideQuantify_normalizing.sh
slideQuantify_tiling.sh
slideQuantify_wrapup.sh

Other scripts

slideToolKitTest.py

Installation

macOSX

Conda version (default/preferred)
Homebrew version

Linux

Rocky 8 Conda version (default/preferred)

Legacy

Ubuntu 16.04 LTS
Ubuntu 12.04 CentOS7 Conda version with modules
Administrator version

Conda vs brew

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