in reply to Re^2: Installation error; INSTALL.pl program is unable to unzip downloaded file
in thread Installation error; INSTALL.pl program is unable to unzip downloaded file

Hi cookersjs. I get the same error log with you. But the reason I faild is the server I work on is network-unavailable. So curl can not download the "release-1-6-924.zip" file(the log is : curl: (6) Couldn't resolve host 'github.com'). Ok! I download the file manually. then run "perl INSTALL.pl", when it goes to : 
Setting up directories
Destination directory ./Bio already exists.
Do you want to overwrite it (if updating VEP this is probably OK) (y/n
+)?

[download]
if I type n, it will exit: 
Setting up directories
Destination directory ./Bio already exists.
Do you want to overwrite it (if updating VEP this is probably OK) (y/n
+)? n
Exiting

[download]
but if I type y, the zip file I download and copy to ./Bio disappear because it will overwrite the ./Bio directory.

I am crazy by this. Could you tell me how to fix this problem? Thanks in advance!

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Re^4: Installation error; INSTALL.pl program is unable to unzip downloaded file
by marto (Cardinal) on Apr 23, 2017 at 07:47 UTC

    BioPerl has dependencies. If you're working 'off line' use a computer that does have internet access to create a minicpan. Transfer this to your server the configure the cpan tool to use this local mirror. It sounds like a lot of work, but it really isn't and will make your life easier in the long run.

[reply]
      Thanks for your reply! But I can not follow you by "Transfer this to your server the configure the cpan tool to use this local mirror", could you give me some details on this? And now I am trying to install all of the dependencies of BioPerl. I wonder whether BioPerl and vep can be installed exactly if the dependencies are all installed... feeling crazy~
[reply]

        Take a look at the installation notes. Note the first suggestion of using your OS package management. Failing that you'll need to meet the dependencies and build from source. cpan/cpanm are command line tools to automate the installation of modules and their dependencies. cpanm is faster and is recommended by the BioPerl installation procedure documented in the link above. Both of these tools require internet access, unless you have a local mirror. My suggestion was to use minicpan on a system with internet access to create a mirror of the cpan, transfer it (via whatever method you use to get files onto this server), the configure cpanm to look at the local mirror rather than try to connect to the internet. For cpanm there is an example in the documentation, the --mirror option, which would be the path to the transferred cpan mirror.

        I use this method at work on a daily basis and have no issues.

        You'll need to spend some time reading and understanding these links. Alternatively speak to your system administrator and have them set this up for you.

[reply]
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