bioexcel / biobb Goto Github PK

sudo docker run -d -t -i -e REDIS_NAMESPACE='staging' \
-e POSTGRES_ENV_POSTGRES_PASSWORD='foo'
-e POSTGRES_ENV_POSTGRES_USER='bar'
-e POSTGRES_ENV_DB_NAME='mysite_staging'
-e POSTGRES_PORT_5432_TCP_ADDR='docker-db-1.hidden.us-east-1.rds.amazonaws.com'
-e SITE_URL='staging.mysite.com'
-p 80:80
--link redis:redis \
--name container_name dockerhub_id/image_name

Hi, I've noticed that all the biobb packages require ==3.7, which I find a bit strict. I was wondering if there're some clear incompatibilities that need to be fixed or if we can expect a change of python requirements to >=3.7 in the near term.
Thanks!

CODE
from biobb_md.gromacs.pdb2gmx import Pdb2gmx

pdbCode = '7kkk'
fixed_pdb = '7kkk_fixed.pdb'

output_pdb2gmx_gro = pdbCode+'_pdb2gmx.gro'
output_pdb2gmx_top_zip = pdbCode+'_pdb2gmx_top.zip'

Pdb2gmx(input_pdb_path=fixed_pdb,
output_gro_path=output_pdb2gmx_gro,
output_top_zip_path=output_pdb2gmx_top_zip).launch()

ERROR
Traceback (most recent call last):
File "/home/zhangxin/ACS/github/BioUtil/BioExcel/const_topol.py", line 24, in
output_top_zip_path=output_pdb2gmx_top_zip).launch()
File "/home/zhangxin/anaconda3/envs/Biobb/lib/python3.7/site-packages/biobb_md/gromacs/pdb2gmx.py", line 45, in init
self.gmx_version = get_gromacs_version(self.gmx_path)
File "/home/zhangxin/anaconda3/envs/Biobb/lib/python3.7/site-packages/biobb_md/gromacs/common.py", line 29, in get_gromacs_version
version = version_str.group(1).strip().replace(".", "")
AttributeError: 'NoneType' object has no attribute 'group'

The code for the fetching and visualization of the PBD structure does not work. This is the tutorial - https://mmb.irbbarcelona.org/biobb/workflows/tutorials/vs_bs

Issues I have identified include

1. The Pdb() function is not downloading any PDB files.
2. The Visualizing 3D structure code also does not accept a pre-defined variable: download_pdb

Can you please fix or send me a link to a website that contains the correct PDB files, so I can visualize any structure?

Hi

I believe you used wrong API docs links in the github readmes:

For example the biobb-amber module has the wrong link: https://biobb_amber.readthedocs.io/en/latest/

The right one is https://biobb-amber.readthedocs.io/en/latest/

I think it is the same for all other modules

Check the PIP and the conda installers for possible dependencies that change the python version.

Also the Python specification should be more specific ie 3.5 or 3.6 or 3.7 instead of just 3

Especially the associated ReadTheDocs: https://biobb.readthedocs.io/en/latest/

Hi,

I just wanted to know if we can install the package with gpu enabled gromacs or amber while standalone gromacs installation is available with gpu I was just wondering if similar thing is available in this package too.

I have been following the tutorial for extracting DNA helical parameters using biobb (link shown below) and ran into a few issues along the way-
https://github.com/bioexcel/biobb_wf_dna_helparms/blob/8a61b23825d7747147aacf6d110cdc8d12c8dce3/biobb_wf_dna_helparms/notebooks/biobb_dna_helparms_tutorial.ipynb

I used GROMACS in order to generate a DNA topology and exported the results of the simulation as a .xtc and .pdb file. The tutorial, however, used .nc and .top file extensions. Thus I tried converting the .xtc file to a .nc file using the mdconvert script (the exact code I used was mdconvert file_name..xtc -o file-_name.nc). This seemed to work. However, I was unable to find a way to generate the DNA topology in the format that was required (i.e. a .top file).

How would you recommend making these GROMACS outputs compatible with your analysis pipeline. Alternatively, do you recommend any changes to the GROMACS set up.

Check pypi installation in README's. Some of them don't work:

https://pypi.org/project/biobb-chemistry/

And others install old versions:

https://pypi.org/project/biobb-analysis/

https://github.com/bioconda/bioconda-utils/blob/master/Dockerfile

biobb_Analysis
biobb_Chemistry

Unify binary names:

chmod u+x $SP_DIR/biobb_analysis/gromacs/cluster.py
cp $SP_DIR/biobb_analysis/gromacs/cluster.py $PREFIX/bin/gmx_cluster

chmod u+x $SP_DIR/biobb_analysis/ambertools/cpptraj_average.py
cp $SP_DIR/biobb_analysis/ambertools/cpptraj_average.py $PREFIX/bin/cpptraj_average

Update Jupyter notebook tutorials:

• Modify import module
• Modify building block name in the execution
• Remove .launch for each of the building blocks