Vaneet Lotay
2016-12-13 19:47:59 UTC
Hello,
I'm trying to install the PrimerDesigner pluging to use primer3 in GBrowse tracks. I followed the instructions for PrimerDesigner which involve installing the Primer3 executable as well as the Bio::PrimerDesigner plugin and everything was installed successfully. Also I added it to the configuration file but I don't see the plugin displayed. The wiki page says that the plugin should be displayed via the 'Reports and Analysis' menu. I don't have the Reports & Analysis text on my GBrowse page but I do have the drop-down bar which has options to download the sequence file, track data as well as others but no Primer option. Is there something I need to activate or configure that I haven't already?
The Wiki page also states that the PrimerDesigner plugin does not work with GBrowse 2.00, I believe my version is about 2.55. So I'm not sure if the Wiki page hasn't been updated yet or the plugin still doesn't work with that GBrowse version? Here are the relevant lines from my conf file:
plugins = FastaDumper SequenceDumper TrackDumper Submitter PrimerDesigner
....
[PrimerDesigner:plugin]
binpath = /usr/local/bin/
method = local
ispcr = http://genome.ucsc.edu/cgi-bin/hgPcr?db=cb3
I only see warnings in my apache error log so not sure if they're relevant to the issue:
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: Base class package "Class::Base" is empty., referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: (Perhaps you need to 'use' the module which defines that package first,, referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: or make that module available in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .)., referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: at /usr/local/share/perl5/Bio/PrimerDesigner/Remote.pm line 32, referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: BEGIN failed--compilation aborted at /usr/local/share/perl5/Bio/PrimerDesigner/Remote.pm line 32., referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: Compilation failed in r, referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: equire at /usr/local/share/perl5/Bio/PrimerDesigner/primer3.pm line 25., referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: BEGIN failed--compilation aborted at /usr/local/share/perl5/Bio/PrimerDesigner/primer3.pm line 25., referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: Compilation failed in require at /usr/local/share/perl5/Bio/PrimerDesigner.pm line 82., referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: BEGIN failed--compilation aborted at /usr/local/share/perl5/Bio/PrimerDesigner.pm line 82., referer: http://test.xenbase.org/entry/
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: Compilation failed in require at /etc/gbrowse2/plugins/PrimerDesigner.pm line 74., referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: BEGIN failed--compilation aborted at /etc/gbrowse2/plugins/PrimerDesigner, referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: .pm line 74., referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: Compilation failed in require at /usr/local/lib64/perl5/Bio/Graphics/Browser2/PluginSet.pm line 31., referer: <host>
I have installed the Class::Base package just so you know. Any help you can provide would be appreciated.
Thanks,
Vaneet
Vaneet Lotay
Xenbase Bioinformatician
403-220-6652
724 ICT Building - University of Calgary
2500 University Drive NW
Calgary AB T2N 1N4
CANADA
I'm trying to install the PrimerDesigner pluging to use primer3 in GBrowse tracks. I followed the instructions for PrimerDesigner which involve installing the Primer3 executable as well as the Bio::PrimerDesigner plugin and everything was installed successfully. Also I added it to the configuration file but I don't see the plugin displayed. The wiki page says that the plugin should be displayed via the 'Reports and Analysis' menu. I don't have the Reports & Analysis text on my GBrowse page but I do have the drop-down bar which has options to download the sequence file, track data as well as others but no Primer option. Is there something I need to activate or configure that I haven't already?
The Wiki page also states that the PrimerDesigner plugin does not work with GBrowse 2.00, I believe my version is about 2.55. So I'm not sure if the Wiki page hasn't been updated yet or the plugin still doesn't work with that GBrowse version? Here are the relevant lines from my conf file:
plugins = FastaDumper SequenceDumper TrackDumper Submitter PrimerDesigner
....
[PrimerDesigner:plugin]
binpath = /usr/local/bin/
method = local
ispcr = http://genome.ucsc.edu/cgi-bin/hgPcr?db=cb3
I only see warnings in my apache error log so not sure if they're relevant to the issue:
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: Base class package "Class::Base" is empty., referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: (Perhaps you need to 'use' the module which defines that package first,, referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: or make that module available in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .)., referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: at /usr/local/share/perl5/Bio/PrimerDesigner/Remote.pm line 32, referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: BEGIN failed--compilation aborted at /usr/local/share/perl5/Bio/PrimerDesigner/Remote.pm line 32., referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: Compilation failed in r, referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: equire at /usr/local/share/perl5/Bio/PrimerDesigner/primer3.pm line 25., referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: BEGIN failed--compilation aborted at /usr/local/share/perl5/Bio/PrimerDesigner/primer3.pm line 25., referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: Compilation failed in require at /usr/local/share/perl5/Bio/PrimerDesigner.pm line 82., referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: BEGIN failed--compilation aborted at /usr/local/share/perl5/Bio/PrimerDesigner.pm line 82., referer: http://test.xenbase.org/entry/
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: Compilation failed in require at /etc/gbrowse2/plugins/PrimerDesigner.pm line 74., referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: BEGIN failed--compilation aborted at /etc/gbrowse2/plugins/PrimerDesigner, referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: .pm line 74., referer: <host>
[Tue Dec 13 12:38:12 2016] [warn] [client 136.159.4.35] mod_fcgid: stderr: Compilation failed in require at /usr/local/lib64/perl5/Bio/Graphics/Browser2/PluginSet.pm line 31., referer: <host>
I have installed the Class::Base package just so you know. Any help you can provide would be appreciated.
Thanks,
Vaneet
Vaneet Lotay
Xenbase Bioinformatician
403-220-6652
724 ICT Building - University of Calgary
2500 University Drive NW
Calgary AB T2N 1N4
CANADA