antoniojbt/project_quickstart

Boilerplate tools and templates for setting up a data analysis project.

project_quickstart's Issues

python xxxx/pipeline_pq_example.py plot full requires dot

For the cgat-core based pipeline, the command:
python ../code/pq_example/pipeline_pq_example/pipeline_pq_example.py plot full

gives:

Traceback (most recent call last):
  File "../code/pq_example/pipeline_pq_example/pipeline_pq_example.py", line 473, in <module>
    sys.exit(P.main(sys.argv))
  File "/opt/conda/envs/pq_test/lib/python3.7/site-packages/cgatcore/pipeline/control.py", line 1390, in main
    run_workflow(options, args)
  File "/opt/conda/envs/pq_test/lib/python3.7/site-packages/cgatcore/pipeline/control.py", line 1286, in run_workflow
    checksum_level=options.ruffus_checksums_level)
  File "/opt/conda/envs/pq_test/lib/python3.7/site-packages/ruffus/task.py", line 4137, in pipeline_printout_graph
    signal_callback=is_node_up_to_date)
  File "/opt/conda/envs/pq_test/lib/python3.7/site-packages/ruffus/graph.py", line 1155, in graph_printout
    retcode, cmd + "\n" + "\n".join([str(result_str), str(error_str)]))
subprocess.CalledProcessError: Command 'dot -Gsize='(11,8)'  -Tsvg < /tmp/tmpy87tn_3t.dot
b''
b'/bin/sh: 1: dot: not found\n'' returned non-zero exit status 127.
(pq_test) root@4782c8cbdd5e:/pq_example/results# dot
bash: dot: command not found

• Add installation instructions

Feedback about example run

Hi Antonio,

Great initiative!

My comments:

• The requirements.rst is not nicely rendered on GitHub and makes it difficult to read:
  https://github.com/AntonioJBT/project_quickstart/blob/master/requirements.rst

Could you please update it?

• When I follow the installation instructions [1] and run pip install git+git://github.com/AntonioJBT/project_quickstart.git, I get:

ModuleNotFoundError: No module named 'future'

You probably want to add future as a pre-requisite.

• When I run project_quickstart --example, I get:

UnicodeEncodeError: 'ascii' codec can't encode characters in position 213-215: ordinal not in range(128)

In our systems, this is solved prepending export LANG=en_GB.UTF-8 to project_quickstart but still I get wrong characters as displayed in [2].

I hope it helps!

Best regards,
Sebastian

[1] Installation steps:

mktemp -d 
cd /tmp/tmp.xDXrlY2ka8
curl -O https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p /tmp/tmp.xDXrlY2ka8/i-1
source i-1/etc/profile.d/conda.sh 
conda activate base
conda install future
pip install git+git://github.com/AntonioJBT/project_quickstart.git

[2] Output of "project_quickstart --example":

Welcome to project_quickstart version 0.3.3 (!).

Path in use:
/tmp/tmp.xDXrlY2ka8/i-1/lib/python3.6/site-packages/templates


Creating the project structure for pq_example in:
/tmp/tmp.xDXrlY2ka8/pq_example


 Done, welcome to pq_example!

        Folders and files have been copied to:
        /tmp/tmp.xDXrlY2ka8/pq_example

        The basic structure is:
                              .
                              ��������� code
                              ��������� data
                              ��������� documents_and_manuscript
                              ��������� results

        Remember to back up code, data and manuscript directories (or your
        equivalents).

        The directory:
        /tmp/tmp.xDXrlY2ka8/pq_example/code

        can be uploaded to a version control system (file templates are for GitHub).
        You could link it to Travis CI, Zenodo and ReadtheDocs for example.
        There are some notes and reminders within the files copied over.
        You may want to change the name 'code' to something more suitable when
        uploading, freezing, packaging, etc.

        Script templates are in:
        /tmp/tmp.xDXrlY2ka8/pq_example/code/pq_example

        The structure largely follows Python packaging conventions.
        You can put scripts, modules and pipelines (eg Ruffus/CGAT, make and Makefiles, etc.)
        in here.

        You can work and save results in:
        /tmp/tmp.xDXrlY2ka8/pq_example/results

        Install Sphinx to render your rst documents in:
        /tmp/tmp.xDXrlY2ka8/pq_example/documents_and_manuscript

        Basic rst template files have been generated already.
        Install and use sphinx-quickstart if you want a more complete skeleton.

        Feel free to raise issues, fork or contribute at:

        https://github.com/AntonioJBT/project_quickstart

        Have fun!

add script_templates to flake8

latexmk and perl conda conflict

Install separate conda environment for building reports to avoid perl and latexmk conflict:

Install latex and requirements for report building:
bash -c 'conda install -y sphinxcontrib-bibtex' # for both pdf and html reports
bash -c 'conda install -y texlive-core latexmk perl-local-lib perl==5.20.3.1' # for pdf reports
latexmk and perl may conflict though (unsatisfiable error...)
latexmk is needed for make latexpdf but needs perl 5.20.3.1
perl-local-lib needs perl > 5.26.2
perl and perl local::lib are needed for latex and sphinx report building, perl without local::lib gives compilation errors and missing modules
This only affects latex and pdf building though, html reports are fine

missing tests

For:

• toy example scripts
• bash pipeline
• cgat pipeline