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galaxyproject / tools-devteam

Contains a set of Galaxy Tools mostly written by the Galaxy Team.
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Kraken2Tax: awk error while loading shared libraries: libreadline.so.6 #599

Closed gmauro closed 2 years ago

gmauro commented 2 years ago

The wrapper is using a tool_shed package to provide the awk binary. The awk binary needs the readline library in a version that is not available anymore.

galaxy@sn06:/usr/local/tools/gnu_awk/4.1.0/iuc/package_gnu_awk_4_1_0/52a8268bb49f/bin$ ./awk
./awk: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory

galaxy@sn06:/usr/local/tools/gnu_awk/4.1.0/iuc/package_gnu_awk_4_1_0/52a8268bb49f/bin$ ldd awk
    linux-vdso.so.1 (0x00007fff7574f000)
    libreadline.so.6 => not found
    libdl.so.2 => /lib64/libdl.so.2 (0x00007fd5d2ea2000)
    libm.so.6 => /lib64/libm.so.6 (0x00007fd5d2b20000)
    libc.so.6 => /lib64/libc.so.6 (0x00007fd5d275e000)
    /lib64/ld-linux-x86-64.so.2 (0x00007fd5d30a6000)
bgruening commented 2 years ago

Can you retry this? I think I fixed it.

bgruening commented 2 years ago

On our server ...

gmauro commented 2 years ago

Nope.

awk: symbol lookup error: /usr/local/tools/gnu_awk/4.1.0/iuc/package_gnu_awk_4_1_0/52a8268bb49f/lib/libreadline.so.6: undefined symbol: PC
bgruening commented 2 years ago

And now? :)

gmauro commented 2 years ago

It works, but, I am not sure that I want to know how you fixed it!

bgruening commented 2 years ago

No worries, I will not tell you ;)