KentUtils installation issue

Question

[tothepoint]

I am trying to install KentUtils on our Linux server. I tried follow this: post but ended with error. unrecognized command line option -fno-plt. I am stuck in the installation step and need to perform pairwise whole genome alignment chaining, netting and axtnet of two species.Any help in this regards will be of great help.

Thanks Devender

[Devon Ryan]

UCSC provides binaries and we ship likely all of kent's tools via bioconda. Have you tried either of those options?

[tothepoint]

I tried installing via bioconda but it says library not found.

[Devon Ryan]

Please post the entire error message.

[tothepoint]

gcc: error: unrecognized command line option '-fno-plt'

make[2]: * [../inc/common.mk:401: aliType.o] Error 1

make[2]: Leaving directory '/680_info4/project/arora/program/kentUtils-master/src/lib'

make[1]: * [makefile:18: topLibs] Error 2

make[1]: Leaving directory '/680_info4/project/arora/program/kentUtils-master/src'

make: * [Makefile:27: libs] Error 2

[GenoMax]

If you are installing via conda you should not need to compile anything. Provide your conda command line.

Kent utils for linux are available here in compiled form, if you are an academic user. Add execute permission after download.

[tothepoint]

I tried by using conda install -c bioconda kentUtils

I got this error:

Error:PackagesNotFoundError: The following packages are not available from current channels:

• kentutils

Current channels:

• https://conda.anaconda.org/bioconda/linux-64
• https://conda.anaconda.org/bioconda/noarch
• https://repo.anaconda.com/pkgs/main/linux-64
• https://repo.anaconda.com/pkgs/main/noarch
• https://repo.anaconda.com/pkgs/r/linux-64
• https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're looking for, navigate to

[GenoMax]

Which exact util are you looking for? As @Devon said above these utilities are available as individual programs but not as a package.

[tothepoint]

This works. I am equally thankful to you all.

Answer 1

[Mensur Dlakic]

Your gcc/g++ version is not recent enough. See here how to fix it.

[tothepoint]

After your recommendation I am trying to update gcc but need some administration privileges. I think this will work.

Answer 2

[Luis Nassar]

Hello,

As mentioned in the linked post, you can download all the compiled binaries for linux directly from the Genome Browser here: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/

You can rsync all of the utilities:

rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/ ./

Or just get specific ones, e.x.

wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/axtChain

If you have any questions regarding the Genome Browser or its utilities, you can email us at [e-mail]. We also do check biostars periodically, in which case using the UCSC tag is the best way for us to find your questions.

[tothepoint]

rsync not copying any file.

[Devon Ryan]

You can click on the link and just download whatever you want.