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Operating Systems Linux Red Hat Add directory to path permanently Post 303024778 by Scott on Tuesday 16th of October 2018 02:59:07 PM
Old 10-16-2018
Perhaps I misread your first post. Did you actually edit your .bashrc to add the path to gatk-4.0.10.1, or just change it on the command line?

(second, probably silly question - are you using bash?).

/root/bin was most likely added to PATH from some default bashrc in /etc, or in .bash_profile in root's home directory.
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PERLBREW(1p)						User Contributed Perl Documentation					      PERLBREW(1p)

NAME
perlbrew - Perl environment manager. SYNOPSIS
perlbrew command syntax: perlbrew <command> [options] [arguments] Commands: init Initialize perlbrew environment. install Install perl uninstall Uninstall the given installation available List perls available to install lib Manage local::lib directories. alias Give perl installations a new name list List perl installations use Use the specified perl in current shell off Turn off perlbrew in current shell switch Permanently use the specified perl as default switch-off Permanently turn off perlbrew (revert to system perl) self-upgrade Upgrade perlbrew itself. install-cpanm Install cpanm, a friendly companion. install-patchperl Install patchperl mirror Pick a preferred mirror site version Display version help Read more detailed instructions Options for "install" command: -f --force Force installation -j $n Parallel buildng and testing. ex. C<perlbrew install -j 5 perl-5.14.2> -n --notest Skip testing --as Install the given version of perl by a name. ex. C<perlbrew install perl-5.6.2 --as legacy-perl> -D,-U,-A Switches passed to perl Configure script. ex. C<perlbrew install perl-5.10.1 -D usemymalloc -U uselargefiles> --sitecustomize $filename Specify a file to be installed as sitecustomize.pl Generic command options: -q --quiet Be quiet on informative output message. -v --verbose Tell me more about it. See `perlbrew help` for the full documentation of perlbrew, or See `perlbrew help <command>` for detail description of the command. INSTALLATION
It is the simpleist to use the perlbrew installer, just paste this statement to your terminal: curl -kL http://install.perlbrew.pl | bash Or this one, if you have "fetch" (default on FreeBSD): fetch -o- http://install.perlbrew.pl | sh After that, "perlbrew" installs itself to "~/perl5/perlbrew/bin", and you should follow the instruction on screen to modify your shell rc file to put it in your PATH. The installed perlbrew command is a standalone executable that can be run with system perl. The minimun system perl version requirement is 5.8.0, which should be good enough for most of the OSes these days. A packed version of "patchperl" to "~/perl5/perlbrew/bin", which is required to build old perls. The directory "~/perl5/perlbrew" will contain all install perl executables, libraries, documentations, lib, site_libs. In the documentation, that directory is referred as "perlbrew root". If you need to set it to somewhere else because, say, your HOME has limited quota, you can do that by setting "PERLBREW_ROOT" environment variable before running the installer: export PERLBREW_ROOT=/opt/perl5 curl -kL http://install.perlbrew.pl | bash You may also install perlbrew from CPAN: cpan App::perlbrew In this case, the perlbrew command is installed as "/usr/bin/perlbrew" or "/usr/local/bin/perlbrew" or others, depending on the location of your system perl installation. Please make sure not to run this with one of the perls brewed with perlbrew. It's the best to turn perlbrew off before you run that, if you're upgrading. perlbrew off cpan App::perlbrew You should always use system cpan (like /usr/bin/cpan) to install "App::perlbrew" because it will be installed under a system PATH like "/usr/bin", which is not affected by perlbrew "switch" or "use" command. The "self-upgrade" command will not upgrade the perlbrew installed by cpan command, but it is also easy to upgrade perlbrew by running `cpan App::perlbrew` again. CONFIGURATION
PERLBREW_ROOT By default, perlbrew builds and installs perls into "$ENV{HOME}/perl5/perlbrew" directory. To use a different directory, set this environment variable in your "bashrc" to the directory in your shell RC before sourcing perlbrew's RC. It is possible to share one perlbrew root with multilpe user account on the same machine. Therefore people do not have to install the same version of perl over an over. Let's say "/opt/perl5" is the directory we want to share. All users should be able append this snippet to their bashrc to make it effective: export PERLBREW_ROOT=/opt/perl5 source ${PERLBREW_ROOT}/etc/bashrc After doing so, everone's PATH should include "/opt/perl5/bin" and "/opt/perl5/perls/${PERLBREW_PERL}/bin". Each user can invoke "perlbrew switch" and "perlbrew use" to independently switch to different perl environment of their choice. However, only the user with write permission to $PERLBREW_ROOT may install CPAN modules. This is both good and bad depending on the working convention of your team. If you wish to install CPAN modules only for yourself, you should use the "lib" command to construct a personal local::lib environment. local::lib environments are personal, and are not shared between different users. For more detail, read "perlbrew help lib" and the documentation of local::lib. If you want even a cooler module isolation and wish to install CPAN modules used for just one project, you should use carton for this purpose. It is also possible to set this variable before installing perlbrew to make perlbrew install itself under the given PERLBREW_ROOT: export PERLBREW_ROOT=/opt/perl5 curl -kL http://install.perlbrew.pl | bash After doing this, the perlbrew executable is installed as "/opt/perl5/bin/perlbrew" PERLBREW_HOME By default, perlbrew stores per-user setting to "$ENV{HOME}/.perlbrew" directory. To use a different directory, set this environment variable in your shell RC before sourcing perlbrew's RC. In some cases, say, your home directory is on NFS and shared across multiple machines, you may wish to have several different perlbrew setting per-machine. To do so, you can use the "PERLBREW_HOME" environment variable to tell perlbrew where to look for the initialization file. Here's a brief bash snippet for the given senario. if [ "$(hostname)" == "machine-a" ]; then export PERLBREW_HOME=~/.perlbrew-a elif [ "$(hostname)" == "machine-b" ]; then export PERLBREW_HOME=~/.perlbrew-b fi source ~/perl5/perlbrew/etc/bashrc COMMAND
: INIT The "init" command should be manually invoked whenever you (the perlbrew user) upgrade perlbrew. However, if the upgrade is done with "self-upgrade" command, or by running the one-line installer manually, this command is invoked automatically. COMMAND
: INSTALL install [ perl-<version> | <version> ] Build and install the given version of perl. Version numbers usually look like "5.x.xx", or "perl-5.xx.x-RCx" for release candidates. The specified perl is downloaded from the offical CPAN website or from the mirror site configured before. To configure mirror site, invoke `mirror` command. install [ perl-blead | blead ] A special way to install the blead version of perl, which is downloaded from this specific URL regardless of mirror settings: http://perl5.git.perl.org/perl.git/snapshot/blead.tar.gz install /path/to/perl/git/checkout/dir Build and install from the given git checkout dir. install /path/to/perl-5.14.0.tar.gz Build and install from the given archive file. install http://example.com/mirror/perl-5.12.3.tar.gz Build and install from the given URL. Supported URL schemes are "http://", "https://", "ftp://" and "file://". COMMAND
: UNINSTALL Usage: perlbrew uninstall <name> Uninstalls the given perl installation. COMMAND
: USE Usage: perlbrew use [perl-<version> | <version> | <name>] Use the given version perl in current shell. This will not effect newly opened shells. Without a parameter, shows the version of perl currently in use. COMMAND
: SWITCH Usage: perlbrew switch [ <name> ] Switch to the given version, and makes it the default for this and all future terminal sessions. Without a parameter, shows the version of perl currently selected. COMMAND
: LIST Usage: perlbrew list List the installed versions of perl. COMMAND
: AVAILABLE Usage: perlbrew available List the recently available versions of perl on CPAN. The list is retrieved from the web page <http://www.cpan.org/src/README.html>, and is not the list of *all* perl versions ever releasesed in the past. NOTICE: This command might be gone in the future and becomes an option of 'list' command. COMMAND
: OFF Usage: perlbrew off Temporarily disable perlbrew in the current shell. Effectively re-enables the default system Perl, whatever that is. This command works only if you add the statement of `source $PERLBREW_ROOT/etc/bashrc` in your shell initialization (bashrc / zshrc). COMMAND
: SWITCH-OFF Usage: perlbrew switch-off Permananently disable perlbrew. Use "switch" command to re-enable it. Invoke "use" command to enable it only in the current shell. Re-enables the default system Perl, whatever that is. COMMAND
: ALIAS Usage: perlbrew alias [-f] create <name> <alias> Create an alias for the installation named <name>. Usage: perlbrew alias [-f] rename <old_alias> <new_alias> Rename the alias to a new name. Usage: perlbrew alias delete <alias> Delete the given alias. COMMAND
: MIRROR Usage: perlbrew mirror Run this if you want to choose a specific CPAN mirror to install the perls from. It will display a list of mirrors for you to pick from. Hit 'q' to cancel the selection. COMMAND
: EXEC Usage: perlbrew exec <command> <args...> Execute command for all perls, one by one. For example, run a Hello program: perlbrew exec perl -e 'print "Hello from $] "' The output depends on your perl installations, and looks like this: perl-5.12.2 ========== Hello word from perl-5.012002 perl-5.12.3 ========== Hello word from perl-5.012003 perl-5.13.10 ========== Hello word from perl-5.013010 perl-5.14.0 ========== Hello word from perl-5.014000 Notice that the command is not executed in parallel. COMMAND
: ENV Usage: perlbrew env <name> Low-level command. Invoke this command to see the list of environment variables that are set by "perlbrew" itself for shell integration. The output is something similar to this (if your shell is bash/zsh): export PERLBREW_ROOT=/Users/gugod/perl5/perlbrew export PERLBREW_VERSION=0.31 export PERLBREW_PATH=/Users/gugod/perl5/perlbrew/bin:/Users/gugod/perl5/perlbrew/perls/current/bin export PERLBREW_PERL=perl-5.14.1 tcsh / csh users shall seens lines of 'setenv' statements instead of `export`. COMMAND
: SYMLINK-EXECUTABLES Usage: perlbrew symlink-executables <name> Low-level command. This command is used to create the "perl" executable symbolic link to, say, "perl5.13.6". This is only required for development version of perls. You don't need to do this unless you have been using old perlbrew to install perls, and you find youself confused because the perl that you just installed appears to be missing after invoking `use` or `switch`. perbrew changes its installation layout since version 0.11, which generades symlinks to executables in a better way. If you just upgraded perlbrew (from 0.11 or earlier versions) and "perlbrew switch" failed to work after you switch to a development release of perl, say, perl-5.13.6, run this command: perlbrew symlink-executables perl-5.13.6 This essentially creates this symlink: ${PERLBREW_ROOT}/perls/perl-5.13.6/bin/perl -> ${PERLBREW_ROOT}/perls/perl-5.13.6/bin/perl5.13.6 Newly installed perls, whether they are development versions or not, does not need manually treatment with this command. COMMAND
: INSTALL-CPANM Usage: perlbrew install-cpanm Install the "cpanm" standalone executable in "$PERLBREW_ROOT/bin". For more rationale about the existence of this command, read <http://www.perlbrew.pl/Perlbrew-and-Friends.html> COMMAND
: INSTALL-PATCHPERL Usage: perlbrew install-patchperl Install the "patchperl" standalone executable in "$PERLBREW_ROOT/bin". This is automaticall invoked if your perlbrew installation is done with the installer, but not with cpan. For more rationale about the existence of this command, read <http://www.perlbrew.pl/Perlbrew-and-Friends.html> COMMAND
: SELF-UPGRADE Usage: perlbrew self-upgrade This command upgrades Perlbrew to its latest version. COMMAND
: SELF-INSTALL Usage: perlbrew self-install NOTICE: You should not need to run this command in your daily routine. This command install perlbrew itself to "$PERLBREW_ROOT/bin". It is intended used by the perlbrew installer. However, you may manually do the following to re-install only the "perlbrew" executable: curl -kL http://get.perlbrew.pl -o perlbrew perl ./perlbrew install It is slightly different from running the perlbrew installer because "patchperl" is not installed in this case. COMMAND
: VERSION Usage: perlbrew version Show the version of perlbrew. COMMAND
: LIB Usage: perlbrew lib create <lib-name> perlbrew lib delete <lib-name> The `lib` command is used to manipulate local::lib roots inside perl installations. Effectively it is similar to `perl -Mlocal::lib=/path/to/lib-name`, but a little bit more than just that. A lib name can be a short name, containing alphanumeric, like 'awesome', or a full name, prefixed by a perl installation name and a '@' sign, for example, 'perl-5.14.2@awesome'. Here are some a brief examples to invoke the `lib` command: # Create libs by name perlbrew lib create nobita perlbrew lib create perl-5.12.3@shizuka perlbrew list # See the list of use/switch targets. # Activate a lib in current shell. perlbrew use perl-5.12.3@nobita perlbrew use perl-5.14.2@nobita # Activate a lib as default. perlbrew switch perl-5.14.2@nobita # Delete the lib perlbrew lib delete nobita perlbrew lib delete perl-5.12.3@shizuka Short lib names are local to current perl. A lib name 'nobita' can refer to 'perl-5.12.3@nobita' or 'perl-5.14.2@nobita', depending on your current perl. When "use"ing or "switch"ing to a lib, always provide the long name. A simple rule: the argument to "use" or "siwtch" command should appear in the output of "perlbrew list". UPGRADE NOTES
If you plan to upgrade "perlbrew" from version 0.16 or order to a recent version, you should do these steps to adjust your perl installations: 1. remove $PERLBREW_ROOT/perls/current if it exists 2. remove symlinks under $PERLBREW_ROOT/perls/bin 3. run C<perlbrew symlink-executables> 4. run C<perlbrew init> 5. run C<perlbrew switch $something> to set your default perl. Or simply run these statements to do so (you might need to change the value of PERLBREW_ROOT): export PERLBREW_ROOT=${HOME}/perl5/perlbrew rm -f $PERLBREW_ROOT/perls/current rm -f `find $PERLBREW_ROOT/perls/bin -type l` perlbrew symlink-executables perlbrew init perlbrew switch perl-5.14.2 # or other ones. Finally, you should add this line to the end of your "~/.bash_profile" or "~/.zshenv" file: source "$HOME/perl5/perlbrew/etc/bashrc" Or if you have differnt PERLBREW_ROOT at, say, "/opt/perl5", add: export PERLBREW_ROOT=/opt/perl5 source "$PERLBREW_ROOT/etc/bashrc" After doing that, you will be good to go. SEE ALSO
App::perlbrew, App::cpanminus, Devel::PatchPerl perl v5.14.2 2012-05-27 PERLBREW(1p)
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