Perl library errors: Centos 7
Shagun Gupta
cd /usr/local/tpp/bin export PERL5LIB=/usr/local/tpp/lib/perl
./test_tpi.pl
Eric Deutsch
Hi Shagan, did you perform the `make install` step? Was TPP actually installed in /usr/local/tpp? Or was it installed somewhere else?
--
You received this message because you are subscribed to the Google Groups "spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discu...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/9de7be5b-82f1-4878-b2c6-ea9e3f46d779%40googlegroups.com.
Shagun Gupta
On Friday, November 22, 2019 at 3:25:50 PM UTC-5, Eric Deutsch wrote:
Hi Shagan, did you perform the `make install` step? Was TPP actually installed in /usr/local/tpp? Or was it installed somewhere else?
From: spctools...@googlegroups.com <spctools...@googlegroups.com> On Behalf Of Shagun Gupta
Sent: Friday, November 22, 2019 11:33 AM
To: spctools-discuss <spctools...@googlegroups.com>
Subject: [spctools-discuss] Perl library errors: Centos 7
Hi
I have been trying to install TPP (Sashimi) on a Centos 7 server. I don't have any issues with make. However, on downloading perl libraries as specified here:
and checking for installation of all with,
I get the warning that the following three libraries (TPP, TPP::StatUtilities and tpplib_perl) are missing. I am not sure how to download them since cpan can't find them by name and ".pm" files are in the folder "/home/tpp/svn/trans_proteomic_pipeline/perl/lib".
--
You received this message because you are subscribed to the Google Groups "spctools-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to spctools...@googlegroups.com.
Eric Deutsch
To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discu...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/2342eaa6-6c80-4ee4-ab43-430bf4379966%40googlegroups.com.
Shagun Gupta
To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/2342eaa6-6c80-4ee4-ab43-430bf4379966%40googlegroups.com.
Eric Deutsch
Okay, well, assuming you’re still getting this error, I would need more information to suggest a next course of action. Can you send the output of this:
cd /home/tpp
ls -al
ls -al lib
ls -al lib/perl
export PERL5LIB=/home/tpp/lib/perl
echo $PERL5LIB
perl -v
cd bin
To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discu...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/bf2b60f9-37b0-4e44-a102-dedeb928ccd9%40googlegroups.com.
Shagun Gupta
total 36
drwx------. 17 tpp tpp 4096 Nov 13 11:10 .
drwxr-xr-x. 8 root root 109 Nov 11 14:45 ..
-rw-------. 1 tpp tpp 2930 Nov 21 14:44 .bash_history
-rw-r--r--. 1 tpp tpp 18 Oct 30 2018 .bash_logout
-rw-r--r--. 1 tpp tpp 193 Oct 30 2018 .bash_profile
-rw-r--r--. 1 tpp tpp 231 Oct 30 2018 .bashrc
drwxr-xr-x. 2 tpp tpp 4096 Nov 11 16:08 bin
drwxrwxr-x. 3 tpp tpp 26 Nov 11 14:43 .cache
drwxr-xr-x. 2 tpp tpp 4096 Nov 11 16:08 cgi-bin
drwxr-xr-x. 2 tpp tpp 4096 Nov 11 16:08 conf
drwxrwxr-x. 3 tpp tpp 26 Nov 11 14:43 .config
drwxrwxr-x. 6 tpp tpp 123 Nov 16 14:07 .cpan
drwxr-xr-x. 6 tpp tpp 204 Nov 11 16:08 html
drwxr-xr-x. 4 tpp tpp 42 Nov 11 16:08 lib
drwxr-xr-x. 12 tpp tpp 189 Nov 11 16:08 lic
drwxr-xr-x. 2 tpp tpp 10 Nov 11 16:08 log
drwxr-xr-x. 4 tpp tpp 42 Nov 11 16:08 man
drwxr-xr-x. 2 tpp tpp 4096 Nov 11 16:08 schema
drwxrwxr-x. 3 tpp tpp 85 Nov 11 14:46 .subversion
drwxrwxr-x. 3 tpp tpp 46 Nov 11 14:46 svn
drwxr-xr-x. 3 tpp tpp 27 Nov 11 16:08 users
ls -al lib gives me:
total 8
drwxr-xr-x. 4 tpp tpp 42 Nov 11 16:08 .
drwx------. 17 tpp tpp 4096 Nov 13 11:10 ..
drwxr-xr-x. 3 tpp tpp 4096 Nov 11 16:08 Mayu
drwxr-xr-x. 3 tpp tpp 69 Nov 11 16:08 perl
ls -al lib/perl gives me:
total 12
drwxr-xr-x. 3 tpp tpp 69 Nov 11 16:08 .
drwxr-xr-x. 4 tpp tpp 42 Nov 11 16:08 ..
drwxr-xr-x. 2 tpp tpp 38 Nov 11 16:08 TPP
-r--r--r--. 1 tpp tpp 4873 Nov 11 16:08 tpplib_perl.pm
-r--r--r--. 1 tpp tpp 1359 Nov 11 16:08 TPP.pm
export PERL5LIB=/home/tpp/lib/perl
echo $PERL5LIB
gives me:
/home/tpp/lib/perl
perl -v gives me:
This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi
(with 39 registered patches, see perl -V for more detail)
Copyright 1987-2012, Larry Wall
Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.
Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl". If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.
cd bin
Now shows me that all the libraries have been installed!
Looks like I might have had an error typing the PERL5LIB pathway. Thanks a lot!
-Shagun
To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/bf2b60f9-37b0-4e44-a102-dedeb928ccd9%40googlegroups.com.
Eric Deutsch
Great! If you can send me your log of what CentOS yum commands you had to run to install prequisites (which are different than the Ubuntu apt commands), I can create a CentOS recipe that would help out some other folks.
Regards,
Eric
To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discu...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/fae53a6f-036e-4782-9e58-605ab4a4999c%40googlegroups.com.