Install Kent Source Archive Binaries

Question

[kacollier]

I need to convert several whole-genome files from .fasta files to .2bit as part of Brandt Faircloth's UCE pipeline.

In it, it is recommended that you use a program from the Kent Source Archive called faToTwoBit, found here: http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/. I can download the associated binary to my working directory using this line of code:

rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/macOSX.x86_64/faToTwoBit ./*

...but when I try to run it, I get this error:

dyld: Library not loaded: /usr/local/opt/freetype/lib/libfreetype.6.dylib
  Referenced from: /Users/melospiza/bin/faToTwoBit
  Reason: image not found

From the error and the information on the page linked above, I assume this is a library issue, as three libraries (listed below) are apparently required to run the program.

• /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 902.1.0)
• /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1281.100.1)
• /usr/lib/libiconv.2.dylib (compatibility version 7.0.0, current version 7.0.0)

However, I'm just not really sure how, or where to install those, or even to check my computer's set of libraries to see which ones I need. Any help you can offer would be greatly appreciated.

[GenoMax]

Are you trying to install on a Big Sur (v.11.x) machine? As you can see from the link posted above those binaries are compiled for macOS Catalina (v.10.15.x). My hunch is the problem is because of that. Have you installed Xcode on your machine along with command line tools?

[kacollier]

Yes- I'm running v.11.2, so that would be Big Sur. I haven't separately installed Xcode, but I do have Homebrew. For whatever reason, I thought I remembered that Homebrew installs at least some of the command line tools as dependencies when you install it.

Another comment also mentioned that they found a method that works with Big Sur, so I'm probably going to try that first.

Answer 1

[GenoMax]

You could try your luck with conda by following directions here: https://anaconda.org/bioconda/ucsc-fatotwobit

Edit: I confirmed that this works with BigSur. Either create a new environment to install or do

conda install -c bioconda ucsc-fatotwobit

You can then run faToTwoBit.

[Ram]

conda is the way to go, IMO. I tried source installing on my HPC and had a lot of problems. I created one conda environment for all ucsc-kent-utils and install whatever I need in there.

[kacollier]

Okay, thanks for that. I hadn't though to use conda, but of course there's a distribution on there. Conda's great.