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rlabduke / MolProbity

Protein and nucleic acid validation service
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Command line tools not working #11

Open naikymen opened 5 years ago

naikymen commented 5 years ago

Hello Here I found notes on how to use the commandline tools. https://github.com/rlabduke/MolProbity/blob/master/doc/command_line_tools.txt

After following the instructions in the README untill step 2, the "executables" in MolProbity/cmdline/ do not work. I am trying to use MolProbity in a Docker container. PHP needed to be installed, and I downloaded version 7.2, but other errors appeared afterwards:

PHP Warning: include_once(/home/MolProbity/config/config.php): failed to open stream: No such file or directory in /home/MolProbity/lib/core.php on line 24

PHP Warning: ini_set(): Headers already sent. You cannot change the session module's ini settings at this time in /home/MolProbity/lib/sessions.php on line 129 PHP Warning: ini_set(): Headers already sent. You cannot change the session module's ini settings at this time in /home/MolProbity/lib/sessions.php on line 130 PHP Warning: ini_set(): Headers already sent. You cannot change the session module's ini settings at this time in /home/MolProbity/lib/sessions.php on line 133 PHP Warning: session_name(): Cannot change session name when headers already sent in /home/MolProbity/lib/sessions.php on line 136 PHP Warning: session_set_save_handler(): Cannot change save handler when headers already sent in /home/MolProbity/lib/sessions.php on line 138 Illegal session ID: ''

A list of requirements and clear instructions is missing in the documentation. I know nothing about PHP. How can i get the command-line tools working?

Best, N

saijananiganesan commented 4 years ago

Is PHP a requirement for running command line tools? If so, this should be stated in the Readme file.

a-r-j commented 4 years ago

Hi, did you figure out a solution to this? I'm running into the same error.

prisant commented 4 years ago

(i) MolProbity code uses PHP 5.x and has not been updated to PHP 7.x. (In most Linux distributions it is possible to install the older PHP revision. (ii) Support has not yet been extended to installs in Docker containers.

prisant commented 4 years ago

Also the commandline tools are being actively worked at the present time and therefore may be not stable in the near future

naikymen commented 4 years ago

Hi! thank you for responding.

Please state these requirements in the readme file or elsewhere in the documentation. Otherwise significant user time might be lost.

I imagine this is also a concern for the developers, since citations can sometimes be important. For instance, MolProbity CLI tools were left out of the project I was working on because of this issue.

balasrini32 commented 2 years ago

Has this been fixed? I run into the same error as well.

@prisant I would be very grateful if you could update us

chrissciwilliams commented 2 years ago

I believe we have finally fixed this issue. Various problems with header creation have been resolved. MolProbity, including commandline tools, should now work on current PHP.

All of the fixes were in the molprobity code, not cctbx or other dependencies. So if your MolProbity installation is recent, you can update by:

  1. delete the molprobity directory found at the same level as build, conda_base, and modules
  2. git clone https://github.com/rlabduke/MolProbity.git molprobity
  3. cd molprobity
  4. run setup.sh

Of course, it is always safest to start a fresh installation and get the latest cctbx code, too.

If you find a cmdline tool that still does not work, please let me know which one.

Thank you for your patience, -Christopher Williams ---Richardson Lab, Duke University

balasrini32 commented 2 years ago

Thank you very much Christopher! It works for me with php 5.6 on conda - via https://anaconda.org/pwwang/php (With versions past 7.4 it still lands into errors with the curly braces etc)