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aces / Loris-MRI

The set of scripts that preprocess and insert MRI data into the database.
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Install process improvements #1105

Open regisoc opened 2 months ago

regisoc commented 2 months ago

Some improvements could be done in the README:

  1. Section 3: MINC install could be updated. We are using Ubuntu (only?) and not following the full MINC install (e.g. no test deb download for the last MINC version), we can add MINC deps at the beginning of section 3. 
    # deps
sudo apt-get install libc6 libstdc++6 imagemagick perl
# visualization
sudo apt-get install libgl1-mesa-glx libglu1-mesa
# download minc deb
# wget beast lib + models lib + main minc lib
# sudo dpkg -i minc-toolkit-<version>.deb bic-mni-models-<version>.deb beast-library-<version>.deb
  2. MINC models should be installed in /opt/minc/share -> need to manually check if it is not empty
  3. running ./install_imaging.sh script, this warning happened. We should run these by default if they are mandatory 
    New CPAN.pm version (v2.36) available.
[Currently running version is v2.28]
You might want to try
install CPAN
reload cpan
to both upgrade CPAN.pm and run the new version without leaving
the current session.
  4. running ./install_imaging.sh, error at the end of the execution. Log:

...

Creating loris-mri Python virtualenv in /opt/Loris-MRI/bin/mri/python_virtualenvs/loris-mri-python/ created virtual environment CPython3.10.12.final.0-64 in 1636ms creator CPython3Posix(dest=/opt/Loris-MRI/bin/mri/python_virtualenvs/loris-mri-python, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/lorisadmin/.local/share/virtualenv) added seed packages: pip==22.0.2, setuptools==59.6.0, wheel==0.37.1 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator Installing the Python libraries into the loris-mri virtualenv... Collecting mne Downloading mne-1.6.1-py3-none-any.whl (8.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.3/8.3 MB 16.4 MB/s eta 0:00:00 Collecting mne-bids>=0.6 Downloading mne_bids-0.14-py2.py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 17.1 MB/s eta 0:00:00 Collecting protobuf>=3.0.0 Downloading protobuf-5.26.1-cp37-abi3-manylinux2014_x86_64.whl (302 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 302.8/302.8 KB 30.2 MB/s eta 0:00:00 Collecting pybids==0.14.0 Using cached pybids-0.14.0-py3-none-any.whl (3.2 MB) Collecting mysqlclient Downloading mysqlclient-2.2.4.tar.gz (90 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 90.4/90.4 KB 12.6 MB/s eta 0:00:00 Installing build dependencies ... done Getting requirements to build wheel ... error error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> [27 lines of output] /bin/sh: 1: pkg-config: not found /bin/sh: 1: pkg-config: not found /bin/sh: 1: pkg-config: not found Trying pkg-config --exists mysqlclient Command 'pkg-config --exists mysqlclient' returned non-zero exit status 127. Trying pkg-config --exists mariadb Command 'pkg-config --exists mariadb' returned non-zero exit status 127. Trying pkg-config --exists libmariadb Command 'pkg-config --exists libmariadb' returned non-zero exit status 127. Traceback (most recent call last): File "/opt/Loris-MRI/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in main() File "/opt/Loris-MRI/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/opt/Loris-MRI/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 130, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-vizsygo0/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 325, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "/tmp/pip-build-env-vizsygo0/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 295, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-vizsygo0/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 311, in run_setup exec(code, locals()) File "", line 155, in File "", line 49, in get_config_posix File "", line 28, in find_package_name Exception: Can not find valid pkg-config name. Specify MYSQLCLIENT_CFLAGS and MYSQLCLIENT_LDFLAGS env vars manually [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error

× Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip. Creating the data directories

Modifying environment script

Creating MRI config file config file is located at /opt/Loris-MRI/bin/mri/dicom-archive/.loris_mri/prod

Creating python database config file with database credentials config file for python import scripts is located at /opt/Loris-MRI/bin/mri/dicom-archive/.loris_mri/database_config.py

Installing DICOM Toolkit (May prompt for sudo password) Reading package lists... Done Building dependency tree... Done Reading state information... Done dcmtk is already the newest version (3.6.6-5). 0 upgraded, 0 newly installed, 0 to remove and 48 not upgraded. Populating database configuration entries for the Imaging Pipeline and LORIS-MRI code and images Path: mysql: [Warning] Using a password on the command line interface can be insecure. mysql: [Warning] Using a password on the command line interface can be insecure. mysql: [Warning] Using a password on the command line interface can be insecure. mysql: [Warning] Using a password on the command line interface can be insecure. mysql: [Warning] Using a password on the command line interface can be insecure. mysql: [Warning] Using a password on the command line interface can be insecure. mysql: [Warning] Using a password on the command line interface can be insecure. mysql: [Warning] Using a password on the command line interface can be insecure.

5. TPCCLIB install needs deps for compiling (needed?). They are general ones. On Ubuntu, we can add them as general deps.
```bash
# build deps
sudo apt install build-essential checkinstall cmake
#
  1. On TPCCLIB website is not easy to read. We can add actual repository link and instructions to ease the pain:

Bonus:

EDIT: this was not working last week. I do not know what changed in between but it works now.

$ ./tools/replicate_raisinbread_for_mcin_dev_vm.pl 
Can't locate NeuroDB/ExitCodes.pm in @INC (you may need to install the NeuroDB::ExitCodes module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.34.0 /usr/local/share/perl/5.34.0 /usr/lib/x86_64-linux-gnu/perl5/5.34 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.34 /usr/share/perl/5.34 /usr/local/lib/site_perl) at ./tools/replicate_raisinbread_for_mcin_dev_vm.pl line 38.
BEGIN failed--compilation aborted at ./tools/replicate_raisinbread_for_mcin_dev_vm.pl line 38.

Linked to #1074

gsch-cmi commented 1 month ago

Can I ask what version of Ubuntu you are testing the install on? I was trying to install on ubuntu noble (24), but it seems like libgl1-mesa-glx is no longer available in 24, and (i think) has been replaced with other packages, e.g. (libglx-mesa0, libglu1-mesa) but i'm not sure if installing these would work for the MRI module tools. Do you have any insight into this and whether documentation could be updated to specify the ubuntu versions for which the install works as specified?