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Update install.md
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kaichop committed May 8, 2015
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Expand Up @@ -78,13 +78,13 @@ If using a very old machine with very old version of make program, the fancy cha

## The last resort

If all the above methods do not work, then you can resort to reinstallation of Perl manually. (Note that sometimes, `perlbrew` cannot correctly compile/install perl even if appropriate arguments were supplied based on their documentation.) This is indeed incredibly simple if you just follow step-by-step instructions below. Suppose that I want to install Perl in `~/usr/perl` directory.
If all the above methods do not work, then you can resort to reinstallation of Perl manually. In fact, I was not able to compile PennCNV in Perl 5.20.2, but was able to compile PennCNV on Perl 5.14.2 and other earlier versions. Although `perlbrew` is commonly used for installing another version of Perl, sometimes `perlbrew` cannot correctly compile/install perl even if appropriate arguments were supplied based on their documentation. So it is best to just install Perl yourself: this is indeed incredibly simple if you just follow step-by-step instructions below. Suppose that I want to install Perl in `~/usr/perl-5.14.2` directory.

```
[kaiwang@biocluster ~/]$ wget http://www.cpan.org/src/perl-5.14.2.tar.gz
[kaiwang@biocluster ~/]$ tar xvfz perl-5.14.2.tar.gz
[kaiwang@biocluster ~/]$ cd perl-5.14.2
[kaiwang@biocluster ~/]$ ./Configure -des -Dprefix=/home/kaiwang/usr/perl -Accflags='-fPIC' -Dusethreads
[kaiwang@biocluster ~/]$ ./Configure -des -Dprefix=/home/kaiwang/usr/perl-5.14.2 -Accflags='-fPIC' -Dusethreads
[kaiwang@biocluster ~/]$ make
[kaiwang@biocluster ~/]$ make test
[kaiwang@biocluster ~/]$ make install
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