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insilichem / tangram

:black_square_button::atom_symbol: A collection of molecular modelling tools for UCSF Chimera
http://tangram-suite.readthedocs.io
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Installation fails on latest ubuntu 18.04.1 fresh iinstall with chimera 1.13 latest stable build #4

Closed pratik-narain closed 5 years ago

pratik-narain commented 6 years ago

This is the error message I receive.

installing: Tangram Suite extensions with pip ... Traceback (most recent call last): File "/home/pratik/tangram/bin/pip", line 7, in <module> from pip._internal import main ImportError: No module named _internal ERROR: executing post_install.sh failed This always happens after the rdkit installation step. Please provide some help or documentation.

jaimergp commented 5 years ago

Hi, this seems to do with a mix between system's pip and Tangram's. I'll try to reproduce your problem with a VM, but in the meantime you can try some of the solutions proposed in this other thread:

https://github.com/pypa/pip/issues/5253

pratik-narain commented 5 years ago

Hello. I have tried the solutions mentioned in the above thread to no avail. My system does not have pip installed so the only pip present is in the tangram executable. I wonder if there is a way to decompress the .sh file and manually change this import line as suggested in the above thread.

jaimergp commented 5 years ago

Hi again! Then, my gut is telling me that this could be solved by creating an updated installer for Tangram. I am currently installing the Ubuntu VM and will report back as soon as I have something functional.

pratik-narain commented 5 years ago

Thank you very much. I am working in a lab where we don't do much in silico work but based on the docs I would very much like to introduce the Tangram suite for our structural analysis.

On Wed 26 Sep, 2018, 4:05 PM Jaime Rodríguez-Guerra, < notifications@github.com> wrote:

Hi again! Then, my gut is telling me that this could be solved by creating an updated installer for Tangram. I am currently installing the Ubuntu VM and will report back as soon as I have something functional.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/insilichem/tangram/issues/4#issuecomment-424667835, or mute the thread https://github.com/notifications/unsubscribe-auth/AT23X95BglcGnOnnCMd5qaMmnMkSLQEDks5ue1htgaJpZM4W1HVq .

jaimergp commented 5 years ago

Hi!

Unfortunately, I cannot reproduce that error and got Tangram to install OK in my VM. These are the steps I followed, in case you want to try:

  1. Downloaded Ubuntu 18.04.1 Desktop and installed it in a new VirtualBox 10GB HDD 4GB RAM Virtual Machine.
  2. Downloaded and installed UCSF Chimera 1.13: cd Downloads; chmod +x chimera* && ./chimera*. All options set to default.
  3. Softlinked chimera binary to ~/.local/bin, nonexisting by default so: mkdir -p ~/.local/bin && ln -s ~/.local/UCSF-Chimera-1.13/bin/chimera ~/.local/bin/chimera.
  4. Added ~/.local/bin to $PATH: echo 'export PATH="~/.local/bin:$PATH"' >> ~/.bashrc. Reopen terminal.
  5. Installed git and cython (for Prody installation): sudo apt install git cython.
  6. Downloaded and installed Tangram 0.0.6 for Linux: bash tangram*.sh.
  7. Followed the instructions at the end of the installer to setup the tangram launcher.

A few warnings might appear, but it is OK (openbabel is not included by default and PLIP complains, but that's normal).

pratik-narain commented 5 years ago

I'll try these tonight and get back to you.

On Wed, Sep 26, 2018 at 5:01 PM Jaime Rodríguez-Guerra < notifications@github.com> wrote:

Hi!

Unfortunately, I cannot reproduce that error and got Tangram to install OK in my VM. These are the steps I followed, in case you want to try:

  1. Downloaded Ubuntu 18.04.1 Desktop and installed it in a new VirtualBox 10GB HDD 4GB RAM Virtual Machine.
  2. Downloaded and installed UCSF Chimera 1.13: cd Downloads; chmod +x chimera && ./chimera. All options set to default.
  3. Softlinked chimera binary to ~/.local/bin, nonexisting by default so: mkdir -p ~/.local/bin && ln -s ~/.local/UCSF-Chimera-1.13/bin/chimera ~/.local/bin/chimera.
  4. Added ~/.local/bin to $PATH: echo 'export PATH="~/.local/bin:$PATH"' >> ~/.bashrc. Reopen terminal.
  5. Installed git and cython (for Prody installation): sudo apt install git cython.
  6. Downloaded and installed Tangram 0.0.6 for Linux: bash tangram*.sh.

A few warnings might appear, but it is OK (openbabel is not included by default and PLIP complains, but that's normal).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/insilichem/tangram/issues/4#issuecomment-424681885, or mute the thread https://github.com/notifications/unsubscribe-auth/AT23X1CbT2i-NMbPvicCoRKXBn-7I2Edks5ue2WrgaJpZM4W1HVq .

pratik-narain commented 5 years ago

Hello. I tried as you suggested on a fresh install of ubuntu. I am still getting the same error. installing: boost-1.56.0-py27_3 ... installing: rdkit-2016.03.4-np111py27_1 ... installing: Tangram Suite extensions with pip ... Traceback (most recent call last): File "/home/pratik/tangram/bin/pip", line 7, in from pip._internal import main ImportError: No module named _internal ERROR: executing post_install.sh failed I'll keep looking for a solution. Thank you.

jaimergp commented 5 years ago

Can you run echo $PATH in your terminal and report the results? Also, for completeness, report the output of env | sort.

jaimergp commented 5 years ago

Hint: $PYTHONPATH might affect the installation. Please try to unset it first.

pratik-narain commented 5 years ago

PATH /home/pratik/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin env | sort

CLUTTER_IM_MODULE=xim COLORTERM=truecolor DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus DESKTOP_SESSION=ubuntu DISPLAY=:0 GDMSESSION=ubuntu GJS_DEBUG_OUTPUT=stderr GJS_DEBUG_TOPICS=JS ERROR;JS LOG GNOME_DESKTOP_SESSION_ID=this-is-deprecated GNOME_SHELL_SESSION_MODE=ubuntu GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/6c360d95_5973_44ae_aaf2_eacea69b8829 GNOME_TERMINAL_SERVICE=:1.100 GPG_AGENT_INFO=/run/user/1000/gnupg/S.gpg-agent:0:1 GTK_IM_MODULE=ibus GTK_MODULES=gail:atk-bridge HOME=/home/pratik IM_CONFIG_PHASE=2 LANG=en_US.UTF-8 LANGUAGE=en_US:en LC_ADDRESS=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8 LC_MEASUREMENT=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_NAME=en_US.UTF-8 LC_NUMERIC=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8 LC_TIME=en_US.UTF-8 LESSCLOSE=/usr/bin/lesspipe %s %s LESSOPEN=| /usr/bin/lesspipe %s LOGNAME=pratik LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36: PAPERSIZE=letter PATH=~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin PWD=/home/pratik/bioinfo QT4_IM_MODULE=xim QT_ACCESSIBILITY=1 QT_IM_MODULE=ibus SESSION_MANAGER=local/pratik-desktop:@/tmp/.ICE-unix/892,unix/pratik-desktop:/tmp/.ICE-unix/892 SHELL=/bin/bash SHLVL=1 SSH_AGENT_PID=985 SSH_AUTH_SOCK=/run/user/1000/keyring/ssh TERM=xterm-256color TEXTDOMAINDIR=/usr/share/locale/ TEXTDOMAIN=im-config USERNAME=pratik USER=pratik _=/usr/bin/env VTE_VERSION=5202 WINDOWPATH=1 XAUTHORITY=/run/user/1000/gdm/Xauthority XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/etc/xdg XDG_CURRENT_DESKTOP=ubuntu:GNOME XDG_DATA_DIRS=/usr/share/ubuntu:/usr/local/share:/usr/share:/var/lib/snapd/desktop XDG_MENU_PREFIX=gnome- XDG_RUNTIME_DIR=/run/user/1000 XDG_SEAT=seat0 XDG_SESSION_DESKTOP=ubuntu XDG_SESSION_ID=1 XDG_SESSION_TYPE=x11 XDG_VTNR=1 XMODIFIERS=@im=ibus

So I got your hint and cleaned up my environment variables as you can see in the env | sort output. Still getting the same error.

jaimergp commented 5 years ago

The variables look OK, so I don't have any more suggestions... :/ If you want, we can arrange a one-on-one remote session so I can further debug it personally, but I understand that it might be not adequate depending on your IT policies. Reach me by email if you are interested: jaime.rodriguezguerra@uab.cat

pratik-narain commented 5 years ago

Well. Can you do anydesk? Or teamviewer?

On Thu 27 Sep, 2018, 8:12 PM Jaime Rodríguez-Guerra, < notifications@github.com> wrote:

The variables look OK, so I don't have any more suggestions... :/ If you want, we can arrange a one-on-one remote session so I can further debug it personally, but I understand that it might be not adequate depending on your IT policies. Reach me by email if you are interested: jaime.rodriguezguerra@uab.cat

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/insilichem/tangram/issues/4#issuecomment-425119157, or mute the thread https://github.com/notifications/unsubscribe-auth/AT23X9gFn0-obeWA3E1K6-79VI4RaIlLks5ufOPKgaJpZM4W1HVq .

jaimergp commented 5 years ago

TeamViewer is perfect.

jaimergp commented 5 years ago

I'll close this since all my tests have been successful for Ubuntu 18.04 and no contact was ever established. Feel free to reopen if needed.