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wurmlab / oswitch

Provides access to complex Bioinformatics software (even BioLinux!) in just one command.
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fails if shell is tcsh #15

Closed qmwugbt112 closed 9 years ago

qmwugbt112 commented 9 years ago

Having got over the sudo problem, I had further issues with the

bundle exec bin/switch biolinux

command.

Here are the last few warning/error messages

Get:5 http://archive.ubuntu.com/ubuntu/ trusty/universe kbuild amd64 1:0.1.9998svn2695+dfsg-1 [539 kB] Get:6 http://archive.ubuntu.com/ubuntu/ trusty/multiverse virtualbox-guest-source all 4.3.10-dfsg-1 [550 kB] debconf: unable to initialize frontend: Dialog debconf: (TERM is not set, so the dialog frontend is not usable.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype dpkg-preconfigure: unable to re-open stdin: Fetched 2,954 kB in 1s (2,122 kB/s) Selecting previously unselected package dkms. (Reading database ... 197222 files and directories currently installed.) Preparing to unpack .../dkms_2.2.0.3-1.1ubuntu5.14.04_all.deb ... Unpacking dkms (2.2.0.3-1.1ubuntu5.14.04) ... Selecting previously unselected package virtualbox-guest-utils. Preparing to unpack .../virtualbox-guest-utils_4.3.10-dfsg-1_amd64.deb ... Unpacking virtualbox-guest-utils (4.3.10-dfsg-1) ... Selecting previously unselected package virtualbox-guest-dkms. Preparing to unpack .../virtualbox-guest-dkms_4.3.10-dfsg-1_all.deb ... Unpacking virtualbox-guest-dkms (4.3.10-dfsg-1) ... Selecting previously unselected package virtualbox-guest-x11. Preparing to unpack .../virtualbox-guest-x11_4.3.10-dfsg-1_amd64.deb ... Unpacking virtualbox-guest-x11 (4.3.10-dfsg-1) ... Selecting previously unselected package kbuild. Preparing to unpack .../kbuild_1%3a0.1.9998svn2695+dfsg-1_amd64.deb ... Unpacking kbuild (1:0.1.9998svn2695+dfsg-1) ... Selecting previously unselected package virtualbox-guest-source. Preparing to unpack .../virtualbox-guest-source_4.3.10-dfsg-1all.deb ... Unpacking virtualbox-guest-source (4.3.10-dfsg-1) ... Processing triggers for man-db (2.6.7.1-1ubuntu1) ... Processing triggers for ureadahead (0.100.0-16) ... Setting up dkms (2.2.0.3-1.1ubuntu5.14.04) ... Setting up virtualbox-guest-utils (4.3.10-dfsg-1) ... Setting up kbuild (1:0.1.9998svn2695+dfsg-1) ... Setting up virtualbox-guest-source (4.3.10-dfsg-1) ... Processing triggers for ureadahead (0.100.0-16) ... Setting up virtualbox-guest-dkms (4.3.10-dfsg-1) ... Loading new virtualbox-guest-4.3.10 DKMS files... First Installation: checking all kernels... dpkg: warning: version '-_' has bad syntax: version number does not start with digit It is likely that 3.16.7-tinycore64 belongs to a chroot's host Setting up virtualbox-guest-x11 (4.3.10-dfsg-1) ... Processing triggers for ureadahead (0.100.0-16) ... Processing triggers for libc-bin (2.19-0ubuntu6.5) ... Giving Google-Chrome a prod, if you have it installed dpkg-query: no packages found matching google-chrome- debconf: unable to initialize frontend: Dialog debconf: (TERM is not set, so the dialog frontend is not usable.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype update-initramfs: deferring update (trigger activated) Processing triggers for initramfs-tools (0.103ubuntu4.2) ... stat: cannot stat ‘/home/’: No such file or directory

All done - your system is updated to Bio-Linux 8! ---> da806f472169 Removing intermediate container 48e963907708 Successfully built da806f472169 Illegal variable name.

yeban commented 9 years ago

Looks like everything went fine till building BioLinux. Issue probably while running the resulting image in a container.

Illegal variable name isn't very helpful. Nothing just before or after that?

What's the output of docker -v?

qmwugbt112 commented 9 years ago

I have just changed my login shell from tcsh to bash and fired up terminal again.

bundle exec bin/switch biolinux now seems to work, without the need for a reinstall. See below

n56-170:~ rnichols$ echo $SHELL /bin/bash n56-170:~ rnichols$ cd switch n56-170:switch rnichols$ boot2docker start Waiting for VM and Docker daemon to start... .o Started. Writing /Users/rnichols/.boot2docker/certs/boot2docker-vm/ca.pem Writing /Users/rnichols/.boot2docker/certs/boot2docker-vm/cert.pem Writing /Users/rnichols/.boot2docker/certs/boot2docker-vm/key.pem

To connect the Docker client to the Docker daemon, please set: export DOCKER_HOST=tcp://192.168.59.103:2376 export DOCKER_CERT_PATH=/Users/rnichols/.boot2docker/certs/boot2docker-vm export DOCKER_TLS_VERIFY=1

n56-170:switch rnichols$ export DOCKER_HOST=tcp://192.168.59.103:2376 n56-170:switch rnichols$ export DOCKER_CERT_PATH=/Users/rnichols/.boot2docker/certs/boot2docker-vm n56-170:switch rnichols$ export DOCKER_TLS_VERIFY=1 n56-170:switch rnichols$ docker run hello-world Hello from Docker. This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:

  1. The Docker client contacted the Docker daemon.
  2. The Docker daemon pulled the "hello-world" image from the Docker Hub. (Assuming it was not already locally available.)
  3. The Docker daemon created a new container from that image which runs the executable that produces the output you are currently reading.
  4. The Docker daemon streamed that output to the Docker client, which sent it to your terminal.

To try something more ambitious, you can run an Ubuntu container with: $ docker run -it ubuntu bash

For more examples and ideas, visit: http://docs.docker.com/userguide/ n56-170:switch rnichols$ cd switch -bash: cd: switch: No such file or directory n56-170:switch rnichols$ ls ..

n56-170:switch rnichols$ sudo gem install bundler Password:

Successfully installed bundler-1.7.12 Parsing documentation for bundler-1.7.12 1 gem installed n56-170:switch rnichols$ bundle install --path .gem Resolving dependencies... Using colorize 0.7.5 Using switch 0.0.1 from source at . Using bundler 1.7.12 Your bundle is complete! It was installed into ./.gem

n56-170:switch rnichols$ bundle exec bin/switch biolinux

################################################################################ You are now running: biolinux, in container: biolinux-5490.

Container is distinct from the shell your launched this container from. Changes you make here will be lost unless it's made to one of the directories below:

It's possible you may not be able to write to one or more directories above, but it should be possible to read data from all. Home directory is often the safest to write to.

Press Ctrl-D or type 'exit' to go back. ################################################################################

rnichols@biolinux-5490:~/switch$ whereis blastall blastall: /usr/bin/blastall /usr/bin/X11/blastall /usr/share/man/man1/blastall.1.gz rnichols@biolinux-5490:~/switch$

yeban commented 9 years ago

That's a bug then. Thanks. Expected behaviour is to give you 'bash', if login shell is not 'bash|zsh|fish'.

yeban commented 9 years ago

Should work with tcsh now. Can you give it a try?

yeban commented 9 years ago

I will close it then. I am able to get it to work if shell is tcsh.

qmwugbt112 commented 9 years ago

Dear Anurag

Did I say, I made my default login shell bash so I can’t test it right away.
I could try and re-engineer the problem if it is vital.

R

Richard Nichols Professor of Genetics http://goo.gl/5oUP2J

On 24 Feb 2015, at 14:37, Anurag Priyam notifications@github.com wrote:

I will close it then. I am able to get it to work if shell is tcsh.

— Reply to this email directly or view it on GitHub.