searchgui tide glibc error

[bernt-matthias]

One of the search engines (tide) seems to need glibc:

/gpfs1/work/songalax/galaxy-dev/database/jobs_directory/005/5277/working/bin/resources/Tide/linux/linux_64bit/crux: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /gpfs1/work/songalax/galaxy-dev/database/jobs_directory/005/5277/working/bin/resources/Tide/linux/linux_64bit/crux)

Unfortunatelly we execute on a cluster system an can not update / change the glibc.

Can this be fixed? Maybe link statically?

see also: bioconda/bioconda-recipes#11000

[hbarsnes]

I'd recommend contacting the Tide developers directly about this. You can do this via the Crux users google group: https://groups.google.com/forum/#!forum/crux-users.

[bernt-matthias]

Dear @hbarsnes I have some ideas on potential solutions: bioconda/bioconda-recipes#11000 .. would be nice to get your feedback.

[hbarsnes]

@bernt-matthias We'd be happy to update the Tide/Crux binaries in SearchGUI as long as this does not reduce the amount of use cases in which Tide can be executed directly from SearchGUI.

Let me know if you manage to come up with a generic solution that seems to work.

[hbarsnes]

@CarlosHorro You did a bit of testing of Tide via SearchGUI on Linux/Mac right? Did you come across this issue as well?

[CarlosHorro]

No, I didn't have that problem when I was testing on Linux & Mac, although I suppose it depends on every software configuration...

[hbarsnes]

@bernt-matthias Can we close this one?

[bernt-matthias]

Ideally we would have the requirements like tide in the conda recipe requirements (currently its only xtandem).

[hbarsnes]

Ok, we'll leave it open then.

[bernt-matthias]

To let you know: the following is available in conda-forge or bioconda:

• Comet https://anaconda.org/bioconda/comet-ms
• makeblastdb https://anaconda.org/bioconda/blast-legacy
• MetaMorpheus https://anaconda.org/conda-forge/metamorpheus
• MSGF https://anaconda.org/bioconda/msgf_plus
• OMSSA https://anaconda.org/bioconda/omssa
• ThermoRawFileParser https://anaconda.org/bioconda/thermorawfileparser
• XTandem https://anaconda.org/bioconda/xtandem

Unavailable so far are:

• Andromeda X
• directag
• 'MS Amanda'
• MyriMatch
• Novor
• Tide

The available might be easily provided by conda given that the required versions are available and that SearchGUI does not use hard coded paths to the binaries. Might be a nice project to replace them step by step. Would also reduce the (conda) package size dramatically.