I will try to include as much info as possible here.
I installed muscle and usearch manually beforehand and tried the ./install.tcsh skip skip option for installation. The installation process failed many times because one or another of the modules would not install. The script tried to force installation but this did not succeed in some instances. I used the following procedure to manually install IO-Pipe-Producer-2.01.tar.gz, Sys-MemInfo-0.98.tar.gz, Math-Random-0.72.tar.gz, and Unix-Processors-2.044.tar.gz :
$ wget http://search.cpan.org/CPAN/authors/id/W/WS/WSNYDER/Unix-Processors-2.044.tar.gz
$ tar xvzf Unix-Processors-2.044.tar.gz
$ cd Unix-Processors-2.044/
$ perl Makefile.PL INSTALL_BASE=/home-3/karoraw1@jhu.edu #My $HOME directory
$ make test
All tests successful.
Files=3, Tests=11, 0 wallclock secs ( 0.05 usr 0.01 sys + 0.11 cusr 0.08 csys = 0.25 CPU)
Result: PASS
$ make install
Running Mkbootstrap for Unix::Processors ()
chmod 644 "Processors.bs"
Manifying 2 pod documents
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /home-3/karoraw1@jhu.edu/lib/perl5/x86_64-linux/auto/Unix/Processors/Processors.so
Installing /home-3/karoraw1@jhu.edu/lib/perl5/x86_64-linux/Unix/Processors.pm
Installing /home-3/karoraw1@jhu.edu/lib/perl5/x86_64-linux/Unix/Processors/Info.pm
Installing /home-3/karoraw1@jhu.edu/man/man3/Unix::Processors.3
Installing /home-3/karoraw1@jhu.edu/man/man3/Unix::Processors::Info.3
Appending installation info to /home-3/karoraw1@jhu.edu/lib/perl5/x86_64-linux/perllocal.podThis allowed installation of CFF to complete, however the test scripts failed. I commented out the sections of run_CFF_on_Fast*.tcsh that were breaking down on the results of the getconf ARG_MAX command. I still couldn't run the example scripts because of an error thrown by the filterIndels.pl command:
Can't locate Unix/Processors.pm in @INC (you may need to install the Unix::Processors module) (@INC contains: /home-3/karoraw1@jhu.edu/perl5/lib/perl5/5.22.0/x86_64-linux /home-3/karoraw1@jhu.edu/perl5/lib/perl5/5.22.0 /home-3/karoraw1@jhu.edu/perl5/lib/perl5/x86_64-linux /home-3/karoraw1@jhu.edu/perl5/lib/perl5 /cm/shared/apps/perl/5.22.0/lib/site_perl/5.22.0/x86_64-linux /cm/shared/apps/perl/5.22.0/lib/site_perl/5.22.0 /cm/shared/apps/perl/5.22.0/lib/5.22.0/x86_64-linux /cm/shared/apps/perl/5.22.0/lib/5.22.0 .).
BEGIN failed--compilation aborted.
I finally got everything to work after I re-installed Unix::Processors using the simpler method:
$ perl -MCPAN -e shell
$ cpan[1]> install Unix::Processors
After this second installation, the ./install.tcsh skip skip command ran through to the end and everything seems to be in order now 👍
This might be an issue that I brought upon myself somehow. I am not familiar with perl at all. I just figured I should let someone know about my struggles.
I will try to include as much info as possible here.
I installed muscle and usearch manually beforehand and tried the
./install.tcsh skip skipoption for installation. The installation process failed many times because one or another of the modules would not install. The script tried to force installation but this did not succeed in some instances. I used the following procedure to manually install IO-Pipe-Producer-2.01.tar.gz, Sys-MemInfo-0.98.tar.gz, Math-Random-0.72.tar.gz, and Unix-Processors-2.044.tar.gz :This allowed installation of CFF to complete, however the test scripts failed. I commented out the sections of
run_CFF_on_Fast*.tcshthat were breaking down on the results of thegetconf ARG_MAXcommand. I still couldn't run the example scripts because of an error thrown by the filterIndels.pl command:I finally got everything to work after I re-installed Unix::Processors using the simpler method:
$ perl -MCPAN -e shell $ cpan[1]> install Unix::ProcessorsAfter this second installation, the
./install.tcsh skip skipcommand ran through to the end and everything seems to be in order now 👍This might be an issue that I brought upon myself somehow. I am not familiar with perl at all. I just figured I should let someone know about my struggles.