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INSaFLU / docker

Easy installation for INSaFLU made by docker
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Problem when update to the last version #12

Open Guasupito opened 1 year ago

Guasupito commented 1 year ago

Hi,

We have an Insaflu installation at FISABIO and we are trying to upgrade to the last version available. But when we are in the building phase we get this error:

_make[1]: Entering directory /software/extra_software/EMBOSS-6.6.0' make[2]: Entering directory/software/extra_software/EMBOSS-6.6.0' make install-exec-hook make[3]: Entering directory /software/extra_software/EMBOSS-6.6.0' /usr/local/bin/embossupdate Check for more recent updates to EMBOSS Error: socket connect failed for database 'EMBOSSupdates': Connection refused Error: ajHttpRead: cannot open HTTP connection 'http://emboss.open-bio.org/updates/EMBOSS.fixes' Died: Failed to read 'http://emboss.open-bio.org/updates/EMBOSS.fixes' EMBOSS release 6.6.0.0: update information not available make[3]: *** [install-exec-hook] Error 1 make[2]: *** [install-exec-am] Error 2 make[3]: Leaving directory/software/extra_software/EMBOSS-6.6.0' make[2]: Leaving directory /software/extra_software/EMBOSS-6.6.0' make[1]: *** [install-am] Error 2 make[1]: Leaving directory/software/extra_software/EMBOSS-6.6.0' make: *** [install-recursive] Error 1 Error installing EMBOSS ERROR: Service 'insaflu-server' failed to build: The command '/bin/sh -c sh /tmpinstall/install.sh' returned a non-zero code: 1

What could be happening?

Kind regards, Guillermo.

INSaFLU commented 1 year ago

Dear Guillermo,

The problem you are reporting should be just a temporary connection issue. I've just built from scratch and I had no problems in the build phase. If you run docker build again it should work.

To minimize these issues, in the future we may provide ready to use virtual machines to download, but we need to think of a way to make it practical given their potential (very large) size.

The installation of the newest 2.0.0-beta version, if you want to use the new viral detection module, is slightly different than before: the build phase is the same, but before running ./up.sh, you first need to run ./up_televir.sh to install all the components of the viral detection module (these can take several hours to install). If you don't run this step the new module will not work, but the previous reference-based module should still work.

If you're updating a previous version to the newest 2.0.0-beta there are small changes that make it incompatible. You will need a specific patch to make it work, which we are currently testing and is not in github yet. Therefore I would recommend if possible to wait a little bit before doing an update of a previous version. I am sorry for the inconvenience.

Kind Regards, Daniel