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You can often right-click to copy the URL of a link on a website and then use |
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How the shell finds executables: $PATH
Now, you might want to tell your login shell that it should look for executable files in this new directory $HOME/local/bin
. This will allow you to use the executable as a one-word command like you are used to:
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login1$ ssaha2
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Instead of writing out the entire path to the executable to run it, like in one of these examples:
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breseq is a tool developed by the Barrick lab. You might use it in a later lesson. It another is a good example of a tool that can be downloaded and compiled.
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breseq uses the common GNU build system install sequence. If you install other GNU tools then the same ./configure; make; make install
command sequence will often be used.
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$login1 cdw $login1 wget http://breseq.googlecode.com/files/breseq-0.17d19.tar.gz $login1 tar -xvzf breseq-0.17d19.tar.gz $login1 cd breseq-0.17d19 $login1 ./configure --prefix=$HOME/local $login1 make $login1 make install |
The extra option --prefix
to ./configure
sets where the executable and any other files associated with the program will be installed. If you leave off this flag, then it will try to install them in a system-side location. You must have administrator privileges to do this and would generally have to substitute sudo make install
for the last step to get this to work. That won't work on TACC! (sudo
means "super-user do".)
For some other tools, the instructions may tell you to skip straight to make
, or you might also have to install some other programs or libraries that the tool you want to use needs to run. Generally, you can find this information in the online documentation or an INSTALL
file in the root of the downloaded code.
Other Cases
In other lessons we'll cover various deviations and elaborations on these two procedures in order to install specific programs, R modules, Perl modules, Python modules, etc.
More Examples
Example: Install the latest version of Bowtie2
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Bowtie2 is comprised of multiple executables. You will need to copy or move all of them into |
Other Cases
In other lessons we'll cover various deviations and elaborations on these two procedures in order to install specific programs, R modules, Perl modules, Python modules, etc.