Run latest docker failed about mysql problem.

[iwangtoknow]

Are you using the latest release? If you are not using the latest release of funannotate, please upgrade, if bug persists then report here. Yes.

docker images
REPOSITORY                TAG                 IMAGE ID            CREATED             SIZE
funannotate               latest              ccafceb711bc        2 hours ago         15.2GB
busco                     latest              74ca66866f16        5 days ago          2.34GB
flye                      2.3.5               64acc6dcbffb        8 days ago          1.04GB
nextgenusfs/funannotate   latest              6dcdab871e87        11 days ago         8.62GB

Describe the bug A clear and concise description of what the bug is. Succeed in building latest docker but failed in running.

...
export FUNANNOTATE_DB=/home/linuxbrew/DB

Removing intermediate container 5f6a5f055b6d
 ---> cea4fd7a0127
Step 10/11 : WORKDIR /home/linuxbrew/data
Removing intermediate container 890177e2e80c
 ---> e5f22fc24191
Step 11/11 : ENTRYPOINT touch $(brew --prefix)/bin/mysql.server &&     sudo chown -R linuxbrew:linuxbrew $(brew --prefix)/bin/mysql $(brew --prefix)/bin/mysqld &&     sudo chmod 777 $(brew --prefix)/bin/mysqld &&     $(brew --prefix)/bin/mysql.server start &&     mysql -uroot -e "CREATE USER 'pasa1'@'localhost' IDENTIFIED BY 'pasa1';" &&     mysql -uroot -e "GRANT ALL PRIVILEGES ON * . * TO 'pasa1'@'localhost';" &&     mysql -uroot -e "FLUSH PRIVILEGES;" &&     /bin/bash
 ---> Running in 552f8053816e
Removing intermediate container 552f8053816e
 ---> ccafceb711bc
Successfully built ccafceb711bc
Successfully tagged funannotate:latest

What command did you issue? Copy/paste the command used. docker build -t funannotate -f Dockerfile . Logfiles Please provide relavent log files of the error.

docker run -it --rm -v /data1/wyq:/home/linuxbrew/data ccafceb711bc
chown: cannot access '/home/linuxbrew/.linuxbrew/bin/mysql': No such file or directory
chown: cannot access '/home/linuxbrew/.linuxbrew/bin/mysqld': No such file or directory

OS/Install Information

• output of funannotate check --show-versions I entered the intermediate container e5f22fc24191 this is the container before ENDPOINT, and checked the dictionary /home/linuxbrew/.linuxbrew/bin/

  linuxbrew@75e431b32593:~/data$ ls /home/linuxbrew/.linuxbrew/bin/
  blast_formatter    gc_cli                python-config
  blastdb_aliastool  gdbm_dump             python2
  blastdbcheck       gdbm_load             python2-config
  blastdbcmd         gdbmtool              python2.7
  blastdbcp          gene_info_reader      python2.7-config
  blastn             idle                  reset
  blastp             infocmp               rmblastn
  blastx             infotocap             rpsblast
  brew               iqtree                rpstblastn
  bunzip2            legacy_blast.pl       run_with_lock
  bzcat              makeblastdb           seedtop
  bzcmp              makembindex           segmasker
  bzdiff             makeprofiledb         seqdb_demo
  bzegrep            mdb_copy              seqdb_perf
  bzfgrep            mdb_dump              smtpd.py
  bzgrep             mdb_load              sqlite3
  bzip2              mdb_stat              tabs
  bzip2recover       mysql.server          tblastx
  bzless             ncurses6-config       test_pcre
  bzmore             ncursesw6-config      tic
  c_rehash           openssl               toe
  captoinfo          patchelf              tput
  clear              pip                   tset
  convert2blastmask  pip2                  update_blastdb.pl
  datatool           pip2.7                wheel
  deltablast         project_tree_builder  windowmasker
  dustmasker         psiblast              windowmasker_2.2.22_adapter.py
  easy_install       pydoc
  easy_install-2.7   python

  And I re-installed mysql with brew in this intermediate container, seems like all be fine. I'm tasting funannotate test WANG

[nextgenusfs]

Sorry about that - I updated the docker-base (dropped mysql because no longer needed) but forgot to push the commit to update the other Docker build file. https://github.com/nextgenusfs/funannotate/commit/8d0e84f7a1d4af340fe9cb207b3902c0f55ebecd

[iwangtoknow]

Oh Jon~