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/etc/profile.d/sra-tools.csh broken #1011

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outpaddling opened this issue Feb 14, 2025 · 0 comments
Open

/etc/profile.d/sra-tools.csh broken #1011

outpaddling opened this issue Feb 14, 2025 · 0 comments

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@outpaddling
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FYI, on RHEL 8, /etc/profile.d/sra-tools.csh is killing the shell startup sequence when LD_LIBRARY_PATH is not set. The command `echo $LD_LIBRARY_PATH' fails, causing the script to terminate, and the shell then does not source ~/.cshrc either. In csh, you need to check for the existence of a variable before trying to reference it:

#version
if ( $?LD_LIBRARY_PATH ) then
    echo $LD_LIBRARY_PATH | /bin/grep -q lib 
    if ( $status != 0 ) setenv LD_LIBRARY_PATH lib:$LD_LIBRARY_PATH
    setenv NGS_LIBDIR lib
endif

This appears to be generated by nstall-root.sh.

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