From e9a790ba148cc3177c35184938a5a096c54ce443 Mon Sep 17 00:00:00 2001 From: Timothy Parnell Date: Tue, 26 Nov 2024 09:51:00 -0700 Subject: [PATCH] small edits --- docs/AdvancedInstallation.md | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/docs/AdvancedInstallation.md b/docs/AdvancedInstallation.md index 7b1922b..f0716de 100644 --- a/docs/AdvancedInstallation.md +++ b/docs/AdvancedInstallation.md @@ -178,10 +178,12 @@ installed. ## 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 @@ -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. @@ -277,7 +279,7 @@ each file. 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;