EDirect Test 12Dec14A
From Bioinformatics.Org Wiki
return to EDirect Perl library dependency problem
Purpose: To test whether Edirect will build and execute on Linux and Mac platforms.
Installation Protocol
cd
mkdir edirect
perl -MNet::FTP -e \
'$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1); $ftp->login;
$ftp->binary; $ftp->get("/entrez/entrezdirect/edirect.zip");'
unzip -u -q edirect.zip
rm edirect.zip
export PATH=$PATH:$HOME/edirect
The next lines copy a pre-built _cpan directory to edirect, that contains all the Perl modules necessary to run CPAN. We cannot count on CPAN being installed on any given system, and the user may not have sysadmin privileges.
cp -p _cpan_template.tar edirect cd edirect tar xvfp _cpan_template.tar mv _cpan_template _cpan rm _cpan_template.tar
At this point, we edit setup.sh to exit before the line reading "if [ ! -e "$HOME/.bashrc" ]". These lines add $HOME/edirect to the $PATH. I have found that lines added to .bashrc and .bash_profile cause the shell to hang when logging in, both using ssh and in a regular GNOME or Xfce session.
./setup.sh
Results:
- Build appears to be successful on all but two systems, both of which have an essentially "out of the box" install of Linux. In both cases, Edirect couldn't find Simple.pm.
- Although all log files end with the same message on all platforms, this appears to occur at different points in the setup procedure. If some components didn't install properly, more in depth testing than just running "einfo" might uncover problems.
| Host | Setup | Execution |
| net30 Scientific Linux 6.5 (RHEL6.5) |
Succeeded. net30.11Dec14.log |
[frist@net30 edirect]$ ./einfo Can't locate LWP/Simple.pm in @INC (@INC contains: /home/frist/edirect/aux/lib/perl5/x86_64-linux-thread-multi /home/frist/edirect/aux/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at ./edirect.pl line 68. BEGIN failed--compilation aborted at ./edirect.pl line 68. |
| orpheus Red Hat Linux 6.6 (RHEL6.6) |
Succeeded. orpheus.17Dec14.log |
{orpheus:/home/brian/edirect}./einfo
Can't locate LWP/Simple.pm in @INC (@INC contains: /home/brian/edirect/aux/lib/perl5/x86_64-linux-thread-multi /home/brian/edirect/aux/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at ./edirect.pl line 68.
BEGIN failed--compilation aborted at ./edirect.pl line 68.
|
| crow CentOS 6.5 (RHEL6.5) |
Succeeded. crow.12Dec14.log |
{crow.cs.umanitoba.ca:/home/other/staff/frist/edirect}./einfo
Must supply -db or -dbs on command line
|
| wotan Fedora 19 (RedHat) |
Succeeded. wotan.11Dec14.log |
{wotan:/home/brian/edirect}./einfo
Must supply -db or -dbs on command line
|
| flamingo Debian 3.2.63-2+deb7ul |
Succeeded. flamingo.12Dec14.log |
frist@flamingo:~/edirect$ ./einfo Must supply -db or -dbs on command line |
| albacore MacOSX - Darwin Kernel Version 10.3.0 |
Succeeded. albacore.11Dec14.log |
{albacore.cs.umanitoba.ca:/Users/frist/edirect}./einfo
Must supply -db or -dbs on command line
|
| peacock MacOSX - Darwin Kernel Version 11.4.2 |
Succeeded. peacock.12Dec14.log Make had returned bad status, install seems impossibleCan't call method "inst_file" on an undefined value at /Users/frist/edirect/setup-deps.pl line 47. |
{albacore.cs.umanitoba.ca:/Users/frist/edirect}./einfo
Must supply -db or -dbs on command line
|
