prokka: home directory is owned by root

[audy]

docker run --entrypoint /bin/ls sjackman/prokka -lash /home

Gives me:

4.0K drwxr-xr-x 11 root root 4.0K Nov 13 14:37 .
4.0K drwxr-xr-x 68 root root 4.0K Jan 29 19:51 ..
4.0K drwxr-xr-x 20 root root 4.0K Nov 13 14:37 linuxbrew

And running sudo asks for a password.

This is odd given that the parent image sjackman/linuxbrew does not.

(note: this is the version on Dockerhub).

[audy]

selab.janelia.org is down for me or I'd try building it myself.

[sjackman]

The last time sjackman/prokka was built was over a year ago. I'll rebuild it now. That should hopefully fix your issue, since it's already resolved in the parent image.

[audy]

Build failed installing infernal. Looks like selab is still down. Do you know of another place to get Infernal? Maybe I can change the homebrew recipe to pull from a GitHub release or something.

[sjackman]

One fix is to upload a copy of the tarball, if you can find one, to some other server (like Bintray) and edit the formula to use that mirror.

[sjackman]

It looks like infernal has moved to http://eddylab.org/software/infernal/infernal-1.1.1.tar.gz

[sjackman]

I've updated the infernal formula. Rebuilding sjackman/prokka.

[sjackman]

BLAST failed to install. I don't have a quick fix for this error. https://hub.docker.com/r/sjackman/prokka/builds/bhxep8hnlalhbq49dv4ze96/

Updating dependency information for /tmp/blast20160130-20924-14k5vwr/ncbi-blast-2.2.31+-src/c++/src/corelib/test_boost.cpp.
/bin/bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
/tmp/blast20160130-20924-14k5vwr/ncbi-blast-2.2.31+-src/c++/src/corelib/test_boost.cpp:73:40: fatal error: boost/test/test_observer.hpp: No such file or directory
 #include <boost/test/test_observer.hpp>
                                        ^
compilation terminated.
FAILED COMMAND:  /usr/bin/g++-4.8  -std=gnu++11 -M  -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE  -isystem/home/linuxbrew/.linuxbrew/include -D_MT -D_REENTRANT -D_THREAD_SAFE -I/tmp/blast20160130-20924-14k5vwr/ncbi-blast-2.2.31+-src/c++/ReleaseMT/inc -I/tmp/blast20160130-20924-14k5vwr/ncbi-blast-2.2.31+-src/c++/include  -Wno-unused-local-typedefs /tmp/blast20160130-20924-14k5vwr/ncbi-blast-2.2.31+-src/c++/src/corelib/test_boost.cpp  | sed ...
make[3]: Leaving directory `/tmp/blast20160130-20924-14k5vwr/ncbi-blast-2.2.31+-src/c++/ReleaseMT/build/corelib'

[sjackman]

The same error has been reported over here: https://bugzilla.redhat.com/show_bug.cgi?id=1259781

[audy]

What do you think about installing BLAST with apt-get instead of Homebrew? Compiling takes forever...

[sjackman]

You could certainly do that on your own system. Remove the blast dependency from prokka, apt-get install blast, and it should work. Linuxbrew will continue to compile BLAST from source.

[audy]

Working on my own Docker image for Prokka.

FYI - Prokka comes bundled with linux binaries for blast, hmmer, prodigal, and aragorn.

[sjackman]

The issue for tracking the BLAST installation error is over here: https://github.com/Homebrew/homebrew-science/issues/2705

[tseemann]

The selab website issue was to do with trnascan which moved websites - this was fixed in the homebrew-science formula.

[sjackman]

I believe that BLAST still doesn't build on Linuxbrew. It would be nice to fix that.