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tjparnell committed Nov 26, 2024
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## Perl modules

Using a simple CPAN package installer such as [CPAN Minus](https://metacpan.org/pod/App::cpanminus),
i.e. `cpanm`, is highly recommended for ease and simplicity in installing modules
from [CPAN](https://metacpan.org). It can install directly from CPAN or take a URL
or downloaded archive file. Other CPAN package managers are available too.
Using a simple CPAN package installer such as [CPAN
Minus](https://metacpan.org/pod/App::cpanminus), i.e. `cpanm`, is highly recommended
for ease and simplicity in installing modules from [CPAN](https://metacpan.org). It
can install directly from CPAN or take a URL or downloaded archive file. Follow the
link to find out how to install `cpanm`. Other CPAN package managers are available
too, if that's your preference.

The following Perl packages should be explicitly installed. Most of these will
bring along a number of dependencies (which in turn bring along more dependencies). In
Expand Down Expand Up @@ -265,7 +267,7 @@ are preferred because they're more efficient and spread the load on modern
multi-CPU environments. You may download these from the UCSC Genome Browser
utilities section for either
[Linux](http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/) or
[macOS](http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/). Copy them to
[macOS](http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.arm64/). Copy them to
your `bin` directory in your `PATH`, for example `$HOME/bin`, `$HOME/perl5/bin`,
or `/usr/local/bin`. Be sure to make them executable by running `chmod +x` on
each file.
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An example for downloading on Linux:

for name in wigToBigWig bedGraphToBigWig bigWigToWig bedToBigBed; \
for name in wigToBigWig bedGraphToBigWig bigWigToWig bigWigToBedGraph bedToBigBed bigBedToBed; \
do curl -o $HOME/bin/$name http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/$name \
&& chmod +x $HOME/bin/$name; done;

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