louisfaure / bulktools-py Goto Github PK

Hi

I am really interested in try this package, I always wanted to run DESeq in python, but I have a doubt, If I have several fastq files from different replicates of each condition. Should I run the bulk pipeline for each fastq file and then merge the adata output? Does the pipeline recognize different fastq file in the folder?

Is there any Jupiter notebook available to see an example?

Thanks

Victor

Hi Louis,

I tried to install the package (using conda as you indicated) and I had the following error:

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for bulktools

Running setup.py clean for bulktools
Failed to build bulktools
Installing collected packages: pytz, commonmark, typing-extensions, six, pyparsing, pygments, numpy, natsort, scipy, rich, python-dateutil, packaging, h5py, pandas, anndata, bulktools
Running setup.py install for bulktools ... error
error: subprocess-exited-with-error

กม Running setup.py install for bulktools did not run successfully.
ฉฆ exit code: 1
จtฉค> [20 lines of output]
running install
/home/victor/miniconda3/envs/bulktools/lib/python3.8/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
creating build
creating build/lib
creating build/lib/bulktools
copying bulktools/init.py -> build/lib/bulktools
copying bulktools/pipeline.py -> build/lib/bulktools
running egg_info
writing bulktools.egg-info/PKG-INFO
writing dependency_links to bulktools.egg-info/dependency_links.txt
writing entry points to bulktools.egg-info/entry_points.txt
writing requirements to bulktools.egg-info/requires.txt
writing top-level names to bulktools.egg-info/top_level.txt
reading manifest file 'bulktools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'bulktools.egg-info/SOURCES.txt'
error: [Errno 2] No such file or directory: 'make'
[end of output]

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

กม Encountered error while trying to install package.
จtฉค> bulktools

Could you give me any advice, please?

Best

Victor